Mouse BAC ends quality assessment and sequence analyses.
A large-scale BAC end-sequencing project at The Institute for Genomic Research (TIGR) has generated one of the most extensive sets of sequence markers for the mouse genome to date. With a sequencing success rate of >80%, an average read length of 485 bp, and ABI3700 capillary sequencers, we have generated 449,234 nonredundant mouse BAC end sequences (mBESs) with 218 Mb total from 257,318 clones from libraries RPCI-23 and RPCI-24, representing 15x clone coverage, 7% sequence coverage, and a marker every 7 kb across the genome. A total of 191,916 BACs have sequences from both ends providing 12x genome coverage. The average Q20 length is 406 bp and 84% of the bases have phred quality scores > or = 20. RPCI-24 mBESs have more Q20 bases and longer reads on average than RPCI-23 sequences. ABI3700 sequencers and the sample tracking system ensure that > 95% of mBESs are associated with the right clone identifiers. We have found that a significant fraction of mBESs contains L1 repeats and approximately 48% of the clones have both ends with > or = 100 bp contiguous unique Q20 bases. About 3% mBESs match ESTs and > 70% of matches were conserved between the mouse and the human or the rat. Approximately 0.1% mBESs contain STSs. About 0.2% mBESs match human finished sequences and > 70% of these sequences have EST hits. The analyses indicate that our high-quality mouse BAC end sequences will be a valuable resource to the community.
Zhao
S
S
The Institute for Genomic Research, Rockville, Maryland 20850, USA. szhao@tigr.org
Shatsman
S
S
Ayodeji
B
B
Geer
K
K
Tsegaye
G
G
Krol
M
M
Gebregeorgis
E
E
Shvartsbeyn
A
A
Russell
D
D
Overton
L
L
Jiang
L
L
Dimitrov
G
G
Tran
K
K
Shetty
J
J
Malek
J A
JA
Feldblyum
T
T
Nierman
W C
WC
Fraser
C M
CM
D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods; D020451:Contig Mapping / Q000379:methods; D020224:Expressed Sequence Tags; D005260:Female; D005822:Genetic Vectors / Q000235:genetics; D016678:Genome; D006801:Humans; D051379:Mice; D008810:Mice, Inbred C57BL; D011786:Quality Control; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods* / Q000592:standards; D016324:Sequence Tagged Sites; D012984:Software