title: 6122023_X61505462_S52_F3R30_R1C3_14C_S52_R1_001

description: positive sample


title: 6122023_X61505438_S128_F7R30_R1C3_14G_S128_R1_001

status: Public on Jul 30 2024

type: SRA

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description: positive sample

library_source: transcriptomic

data_processing:
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BCrpt_count_table.txt; run31_R1BCrpt_count_table.txt; run38_R1BCrpt_count_table.txt; run46_R1BCrpt_count_table.txt; run139_R1BCrpt_count_table.txt; run141p3_R1BCrpt_count_table.txt; run141p6_R1BCrpt_count_table.txt
Supplementary files format and content: run27_R2BCrpt_count_table.txt; run31_R2BCrpt_count_table.txt; run38_R2BCrpt_count_table.txt; run46_R2BCrpt_count_table.txt; run139_R2BCrpt_count_table.txt; run141p3_R2BCrpt_count_table.txt; run141p6_R2BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_count_table.txt; run31_BCrpt_count_table.txt; run38_BCrpt_count_table.txt; run46_BCrpt_count_table.txt; run139_BCrpt_count_table.txt; run141p3_BCrpt_count_table.txt; run141p6_BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_pair_analysis_filenames.txt; run31_BCrpt_pair_analysis_filenames.txt; run38_BCrpt_pair_analysis_filenames.txt; run46_BCrpt_pair_analysis_filenames.txt; run139_BCrpt_pair_analysis_filenames.txt; run141p3_BCrpt_pair_analysis_filenames.txt; run141p6_BCrpt_pair_analysis_filenames.txt

molecule: total RNA

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
Other: RNAseq with limited amplicons.

tag: tissue

value: human nasopharyngeal swab

tag: bc run_id

tag: pipeline version

value: BC


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description: positive sample


title: 6122023_X61505407_S90_F5R30_R1C3_14E_S90_R1_001

description: positive sample


title: 6122023_X61504828_S134_F7R36_R1C3_20G_S134_R1_001

description: positive sample


title: 6122023_X61505474_S204_F11R30_R1C3_14K_S204_R1_001

description: positive sample


title: 6122023_X61504839_S172_F9R36_R1C3_20I_S172_R1_001

description: positive sample


title: 6122023_X61504829_S20_F1R36_R1C3_20A_S20_R1_001

description: positive sample


title: 6122023_X61505574_S242_F13R30_R1C3_14M_S242_R1_001

description: positive sample


title: 6122023_X61504823_S248_F13R36_R1C3_20M_S248_R1_001

description: positive sample


title: 6122023_X61505075_S145_F8R24_R1C3_8H_S145_R1_001

description: positive sample


title: 6122023_X61504827_S58_F3R36_R1C3_20C_S58_R1_001

description: positive sample


title: 6122023_X61504741_S244_F13R32_R1C3_16M_S244_R1_001

description: positive sample


title: 6122023_X61504568_S18_F1R34_R1C3_18A_S18_R1_001

description: positive sample


title: 6122023_X61503961_S35_F2R31_R1C3_15B_S35_R1_001

description: positive sample


title: 6122023_X61504622_S132_F7R34_R1C3_18G_S132_R1_001

description: positive sample


title: 6122023_X61503874_S170_F9R34_R1C3_18I_S170_R1_001

description: positive sample


title: 6122023_X61504477_S210_F11R36_R1C3_20K_S210_R1_001

description: positive sample


title: 6122023_X61503805_S140_F8R19_R1C3_3H_S140_R1_001

description: positive sample


title: 6122023_X61503765_S281_F15R32_R1C3_16O_S281_R1_001

description: positive sample


title: 6122023_X61503694_S94_F5R34_R1C3_18E_S94_R1_001

description: positive sample


title: 6122023_X61504621_S283_F15R34_R1C3_18O_S283_R1_001

description: positive sample


title: 6122023_X61503951_S190_F10R37_R1C3_21J_S190_R1_001

description: positive sample


title: 6122023_X61503680_S263_F14R33_R1C3_17N_S263_R1_001

description: positive sample


title: 6122023_X61505589_S166_F9R30_R1C3_14I_S166_R1_001

description: positive sample


title: 6122023_X61505107_S168_F9R32_R1C3_16I_S168_R1_001

description: positive sample


title: 6122023_X61504882_S285_F15R36_R1C3_20O_S285_R1_001

description: positive sample


title: 6122023_X61505028_S183_F10R24_R1C3_8J_S183_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61503547_S262_F14R31_R1C3_15N_S262_R1_001

description: positive sample


title: 6122023_X61502698_S212_F11R38_R1C3_22K_S212_R1_001

description: positive sample


title: 6122023_X61503667_S36_F2R33_R1C3_17B_S36_R1_001

description: positive sample


title: 6122023_X61502693_S22_F1R38_R1C3_22A_S22_R1_001

description: positive sample


title: 6122023_X61502742_S101_F6R18_R1C3_2F_S101_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61502741_S208_F11R34_R1C3_18K_S208_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61504050_S149_F8R31_R1C3_15H_S149_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61502640_S25_F2R18_R1C3_2B_S25_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61502653_S63_F4R18_R1C3_2D_S63_R1_001

description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61502648_S60_F3R38_R1C3_22C_S60_R1_001

description: positive sample


title: 6122023_X61502349_S196_F11R22_R1C3_6K_S196_R1_001

description: positive sample


title: 6122023_X61502360_S158_F9R22_R1C3_6I_S158_R1_001

description: positive sample


title: 6122023_X61502155_S131_F7R33_R1C3_17G_S131_R1_001

description: positive sample


title: 6122023_X61501971_S86_F5R26_R1C3_10E_S86_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61501897_S48_F3R26_R1C3_10C_S48_R1_001

description: positive sample


title: 6122023_X61501909_S10_F1R26_R1C3_10A_S10_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500748_S12_F1R28_R1C3_12A_S12_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500716_S93_F5R33_R1C3_17E_S93_R1_001

description: positive sample


title: 6122023_X61500746_S47_F3R25_R1C3_9C_S47_R1_001

description: positive sample


title: 6122023_X61502755_S250_F13R38_R1C3_22M_S250_R1_001

description: positive sample


title: 6122023_X61500671_S49_F3R27_R1C3_11C_S49_R1_001

description: positive sample


title: 6122023_X61500668_S50_F3R28_R1C3_12C_S50_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500660_S113_F6R35_R1C3_19F_S113_R1_001

description: positive sample


title: 6122023_X61500663_S200_F11R26_R1C3_10K_S200_R1_001

description: positive sample


title: 6122023_X61500661_S112_F6R33_R1C3_17F_S112_R1_001

description: positive sample


title: 6122023_X61500656_S85_F5R25_R1C3_9E_S85_R1_001

description: positive sample


title: 6122023_X61500648_S161_F9R25_R1C3_9I_S161_R1_001

description: positive sample


title: 6122023_X61500650_S275_F15R26_R1C3_10O_S275_R1_001

description: positive sample


title: 6122023_X61500647_S87_F5R27_R1C3_11E_S87_R1_001

description: positive sample


title: 6122023_X61500644_S77_F5R17_R1C3_1E_S77_R1_001

description: positive sample


title: 6122023_X61500652_S117_F7R19_R1C3_3G_S117_R1_001

description: positive sample


title: 6122023_X61500654_S114_F6R37_R1C3_21F_S114_R1_001

description: positive sample


title: 6122023_X61500591_S256_F14R21_R1C3_5N_S256_R1_001

description: positive sample


title: 6122023_X61500645_S125_F7R27_R1C3_11G_S125_R1_001

description: positive sample


title: 6122023_X61500585_S147_F8R27_R1C3_11H_S147_R1_001

description: positive sample


title: 6122023_X61500526_S229_F13R17_R1C3_1M_S229_R1_001

description: positive sample


title: 6122023_X61500641_S157_F9R21_R1C3_5I_S157_R1_001

description: positive sample


title: 6122023_X61500643_S81_F5R21_R1C3_5E_S81_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500589_S216_F12R19_R1C3_3L_S216_R1_001

description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500504_S155_F9R19_R1C3_3I_S155_R1_001

description: positive sample


title: 6122023_X61500520_S115_F7R17_R1C3_1G_S115_R1_001

description: positive sample


title: 6122023_X61500467_S15_F1R31_R1C3_15A_S15_R1_001

description: positive sample


title: 6122023_X61500491_S83_F5R23_R1C3_7E_S83_R1_001

description: positive sample


title: 6122023_X61500479_S191_F11R17_R1C3_1K_S191_R1_001

description: positive sample


title: 6122023_X61500462_S144_F8R23_R1C3_7H_S144_R1_001

description: positive sample


title: 6122023_X61500487_S261_F14R29_R1C3_13N_S261_R1_001

description: positive sample


title: 6122023_X61500475_S95_F5R35_R1C3_19E_S95_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500464_S146_F8R25_R1C3_9H_S146_R1_001

description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500470_S17_F1R33_R1C3_17A_S17_R1_001

description: positive sample


title: 6122023_X61500450_S302_F16R35_R1C3_19P_S302_R1_001

description: positive sample


title: 6122023_X61500458_S148_F8R29_R1C3_13H_S148_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500408_S76_F4R37_R1C3_21D_S76_R1_001

description: positive sample


title: 6122023_X61500443_S5_F1R21_R1C3_5A_S5_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500472_S39_F3R17_R1C3_1C_S39_R1_001

description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500449_S303_F16R37_R1C3_21P_S303_R1_001

description: positive sample


title: 6122023_X61500338_S38_F2R37_R1C3_21B_S38_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61500332_S214_F12R17_R1C3_1L_S214_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500257_S284_F15R35_R1C3_19O_S284_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61500406_S188_F10R33_R1C3_17J_S188_R1_001

description: positive sample


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description: positive sample


title: 6122023_X61409841_S282_F15R33_R1C3_17O_S282_R1_001

description: positive sample


title: 6122023_X61409822_S272_F15R23_R1C3_7O_S272_R1_001

description: positive sample


title: 6122023_X61409820_S231_F13R19_R1C3_3M_S231_R1_001

description: positive sample


title: 6122023_X61409816_S237_F13R25_R1C3_9M_S237_R1_001

description: positive sample


title: 6122023_X61409821_S274_F15R25_R1C3_9O_S274_R1_001

description: positive sample


title: 6122023_X61409772_S9_F1R25_R1C3_9A_S9_R1_001

description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61409814_S167_F9R31_R1C3_15I_S167_R1_001

description: positive sample


title: 6122023_X61409032_S6_F1R22_R1C3_6A_S6_R1_001

description: positive sample


title: 6122023_X61408955_S106_F6R23_R1C3_7F_S106_R1_001

description: positive sample


title: 6122023_X61408017_S127_F7R29_R1C3_13G_S127_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61407665_S19_F1R35_R1C3_19A_S19_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6122023_X61407257_S8_F1R24_R1C3_8A_S8_R1_001

description: positive sample


title: 6122023_X61407246_S28_F2R21_R1C3_5B_S28_R1_001

description: positive sample


title: 6122023_X61409024_S66_F4R21_R1C3_5D_S66_R1_001

description: positive sample


title: 6122023_X61409819_S266_F15R17_R1C3_1O_S266_R1_001

description: positive sample


title: 6122023_X61407149_S273_F15R24_R1C3_8O_S273_R1_001

description: positive sample


title: 6122023_X61407213_S14_F1R30_R1C3_14A_S14_R1_001

description: positive sample


title: 6122023_X61407146_S84_F5R24_R1C3_8E_S84_R1_001

description: positive sample


title: 6122023_X61407171_S88_F5R28_R1C3_12E_S88_R1_001

description: positive sample


title: 6122023_X61407133_S232_F13R20_R1C3_4M_S232_R1_001

description: positive sample


title: 6122023_X61407128_S300_F16R31_R1C3_15P_S300_R1_001

description: positive sample


title: 6122023_X61407103_S235_F13R23_R1C3_7M_S235_R1_001

description: positive sample


title: 6122023_X61407053_S42_F3R20_R1C3_4C_S42_R1_001

description: positive sample


title: 6122023_X61406985_S79_F5R19_R1C3_3E_S79_R1_001

description: positive sample


title: 6122023_X61407266_S298_F16R27_R1C3_11P_S298_R1_001

description: positive sample


title: 6122023_X61407057_S271_F15R22_R1C3_6O_S271_R1_001

description: positive sample


title: 6122023_X61406843_S301_F16R33_R1C3_17P_S301_R1_001

description: positive sample


title: 6122023_X61406855_S234_F13R22_R1C3_6M_S234_R1_001

description: positive sample


title: 6122023_X61406771_S119_F7R21_R1C3_5G_S119_R1_001

description: positive sample


title: 6122023_X61406797_S193_F11R19_R1C3_3K_S193_R1_001

description: positive sample


title: 6122023_X61406828_S299_F16R29_R1C3_13P_S299_R1_001

description: positive sample


title: 6122023_X61406819_S7_F1R23_R1C3_7A_S7_R1_001

description: positive sample


title: 6122023_X61406743_S41_F3R19_R1C3_3C_S41_R1_001

description: positive sample


title: 6122023_X61406737_S51_F3R29_R1C3_13C_S51_R1_001

description: positive sample


title: 6122023_X61406615_S236_F13R24_R1C3_8M_S236_R1_001

description: positive sample


title: 6122023_X61406740_S43_F3R21_R1C3_5C_S43_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6292023_W82503400_S38_F2R30_R1C3_14B_S401_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6292023_W82503075_S306_F14R27_R1C3_11N_S669_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6292023_W82502345_S180_F8R36_R1C3_20H_S543_R1_001

description: positive sample


title: 6292023_W82502342_S86_F4R32_R1C3_16D_S449_R1_001

description: positive sample


title: 6292023_W82502337_S110_F5R34_R1C3_18E_S473_R1_001

description: positive sample


title: 6292023_W82502335_S200_F9R34_R1C3_18I_S563_R1_001

description: positive sample


title: 6292023_W82502309_S315_F14R36_R1C3_20N_S678_R1_001

description: positive sample


title: 6292023_W82502310_S92_F4R38_R1C3_22D_S455_R1_001

description: positive sample


title: 6292023_W82502305_S291_F13R35_R1C3_19M_S654_R1_001

description: positive sample


title: 6292023_W82502317_S109_F5R33_R1C3_17E_S472_R1_001

description: positive sample


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description: positive sample


title: 6292023_W82502331_S256_F12R22_R1C3_6L_S619_R1_001

description: positive sample


title: 6292023_W82502289_S318_F15R17_R1C3_1O_S681_R1_001

description: positive sample


title: 6292023_W82502273_S218_F10R29_R1C3_13J_S581_R1_001

description: positive sample


title: 6292023_W82502270_S226_F10R37_R1C3_21J_S589_R1_001

description: positive sample


title: 6292023_W82502263_S299_F14R20_R1C3_4N_S662_R1_001

description: positive sample


title: 6292023_W82502261_S167_F8R23_R1C3_7H_S530_R1_001

description: positive sample


title: 6292023_W82502251_S209_F10R20_R1C3_4J_S572_R1_001

description: positive sample


title: 6292023_W82502233_S314_F14R35_R1C3_19N_S677_R1_001

description: positive sample


title: 6292023_W82502269_S33_F2R25_R1C3_9B_S396_R1_001

description: positive sample


title: 6292023_W82502226_S45_F2R37_R1C3_21B_S408_R1_001

description: positive sample


title: 6292023_W82502225_S207_F10R18_R1C3_2J_S570_R1_001

description: positive sample


title: 6292023_W82502229_S119_F6R20_R1C3_4F_S482_R1_001

description: positive sample


title: 6292023_W82502196_S68_F3R38_R1C3_22C_S431_R1_001

description: positive sample


title: 6292023_W82502201_S339_F15R38_R1C3_22O_S702_R1_001

description: positive sample


title: 6292023_W82502192_S76_F4R22_R1C3_6D_S439_R1_001

description: positive sample


title: 6292023_W82502190_S296_F14R17_R1C3_1N_S659_R1_001

description: positive sample


title: 6292023_W82502186_S202_F9R36_R1C3_20I_S565_R1_001

description: positive sample


title: 6292023_W82502170_S157_F7R36_R1C3_20G_S520_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


title: 6292023_W73008163_S44_F2R37_R3C3_21B_S44_R1_001

description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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description: positive sample


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