title: Complete Genome Sequence GS01682-DNA_H04
design: WARNING: UCV (unusual coverage variation) genome with the following QC observations: 1) There is more variability in 100kb coverage windows than we generally see for normal genomes. The number of CNV segments, the total number of CNV bases, and the rates of novel CNVs are also high. Together these data suggest a reduction in the quality of CNV calls. 2) The list of all identified junctions (adjacent regions in the sample genome that are not adjacent in the reference genome) in the sample genome is enriched for short range strand-inverted calls (SIRS). Previous experience suggests that these SIRS are enriched for errors. In contrast, the list of junctions filtered for high confidence criteria looks completely normal and is unaffected by this issue. If it would be helpful, we can provide you with tools to filter SIRS junctions from the allJunctions file and instructions to regenerate the SvEvents files using this filtered data set. We believe these files should be depleted for false positive junctions and events. 3) We see an increase in the number of reference-biased novel SNP calls in repeat regions. These are novel SNP calls in loci where the alt allele frequency is <<0.5 and which are located in repeat regions (e.g. Alu repeats). In other genomes we have observed with this phenomenon, the majority (~75%) of such SNPs are in half-called regions where one allele is no-called. If it would be helpful, we can provide an updated masterVar file where we have converted suspicious calls (located in repeat, alt allele fraction is <<0.5) to our VQLOW VarQuality score.  Note again that these SNPs are in repeat regions and calls outside repeats are unlikely to be affected. 4) Statistics measuring the quality of MEI calls look completely normal.
attributes.tag: Gaps Table
attributes.value: id type armId indArm objArm min max|0 read 0 0 0 5 5|1 gap 0 1 0 -4 -1|2 read 0 2 1 10 10|3 gap 0 3 1 0 3|4 read 0 4 2 10 10|5 gap 0 5 2 3 8|6 read 0 6 3 10 10|7 mategap 0 7 0 100 700|8 read 1 0 0 10 10|9 gap 1 1 0 3 8|10 read 1 2 1 10 10|11 gap 1 3 1 0 3|12 read 1 4 2 10 10|13 gap 1 5 2 -4 -1|14 read 1 6 3 5 5