1@HD VN:1.5 SO:coordinate 2@SQ SN:chrM LN:16299 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:11c8af2a2528b25f2c080ab7da42edda SP:Mus musculus 3@SQ SN:chr1 LN:197195432 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:f05d753079c455c0e57af88eeda24493 SP:Mus musculus 4@SQ SN:chr2 LN:181748087 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:9b9d64dc89ecc73d3288eb38af3f94bd SP:Mus musculus 5@SQ SN:chr3 LN:159599783 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:0a692666a1b8526e1d1e799beb71b6d0 SP:Mus musculus 6@SQ SN:chr4 LN:155630120 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:f5993a04396a06ed6b28fa42b2429be0 SP:Mus musculus 7@SQ SN:chr5 LN:152537259 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:f90804fb8fe9cb06076d51a710fb4563 SP:Mus musculus 8@SQ SN:chr6 LN:149517037 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:258a37e20815bb7e3f2e974b9d4dd295 SP:Mus musculus 9@SQ SN:chr7 LN:152524553 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:e0d6cea6f72cb4d9f8d0efc1d29dd180 SP:Mus musculus 10@SQ SN:chr8 LN:131738871 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:5f217cb8a9685b9879add3ae110cabd7 SP:Mus musculus 11@SQ SN:chr9 LN:124076172 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:dde08574942fc18050195618cc3f35af SP:Mus musculus 12@SQ SN:chr10 LN:129993255 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:be7e6a13cc6b9da7c1da7b7fc32c5506 SP:Mus musculus 13@SQ SN:chr11 LN:121843856 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:e0099550b3d3943fb9bb7af6fa6952c1 SP:Mus musculus 14@SQ SN:chr12 LN:121257530 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:1f9c11dc6f288f93e9fab56772a36e85 SP:Mus musculus 15@SQ SN:chr13 LN:120284312 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:a7b4bb418aa21e0ec59d9e2a1fe1810b SP:Mus musculus 16@SQ SN:chr14 LN:125194864 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:09d1c8449706a17d40934302a0a3b671 SP:Mus musculus 17@SQ SN:chr15 LN:103494974 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:e41c8b42b0921378b1fdd5172f6be067 SP:Mus musculus 18@SQ SN:chr16 LN:98319150 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:e051b3930c2557ade21d67db41f3a518 SP:Mus musculus 19@SQ SN:chr17 LN:95272651 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:47eede15e5761fb9c2267627f18211e7 SP:Mus musculus 20@SQ SN:chr18 LN:90772031 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:9f9d41cfdb9d91b62b928a3eb4eb6928 SP:Mus musculus 21@SQ SN:chr19 LN:61342430 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:591f8486f82c22442bb8463595a18e0a SP:Mus musculus 22@SQ SN:chrX LN:166650296 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:3d0d9df898d2c830b858f91255d8a1eb SP:Mus musculus 23@SQ SN:chrY LN:15902555 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:5ff564f9fbc8cb87bcad6cfa6874902b SP:Mus musculus 24@SQ SN:chr1_random LN:1231697 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:801e0bcd6ae33eeddfe2a4e6fc9f3d36 SP:Mus musculus 25@SQ SN:chr3_random LN:41899 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:d6340e90da5796b7069708735f82ae3e SP:Mus musculus 26@SQ SN:chr4_random LN:160594 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:af94651d419f27e242d0f82d6d5dbe67 SP:Mus musculus 27@SQ SN:chr5_random LN:357350 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:c2db94dc571b1a7cd12eb98564c9fd1e SP:Mus musculus 28@SQ SN:chr7_random LN:362490 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:b1f2189dd882e9c21cdbbf57ba85f4fe SP:Mus musculus 29@SQ SN:chr8_random LN:849593 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:3b0dfe8c89728afd327e229037570f6e SP:Mus musculus 30@SQ SN:chr9_random LN:449403 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:b9845732324c3c38b767a7652410068f SP:Mus musculus 31@SQ SN:chr13_random LN:400311 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:0ef638f43ade721b3aed0386dc8aa4cf SP:Mus musculus 32@SQ SN:chr16_random LN:3994 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:eb0fc598242fe03d53021929cea74c6b SP:Mus musculus 33@SQ SN:chr17_random LN:628739 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:f5a3fcd550c795e0a1bc3f355bb54577 SP:Mus musculus 34@SQ SN:chrX_random LN:1785075 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:3a45dd9ba2fbba51c13d600585ebed09 SP:Mus musculus 35@SQ SN:chrY_random LN:58682461 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:5cbfdcc893c1417a651fc2f3c5732e6a SP:Mus musculus 36@SQ SN:chrUn_random LN:5900358 UR:ftp://hgdownload.cse.ucsc.edu/goldenPath/Mus_musculus_assembly9/bigZips/chromFa.tar.gz AS:mm9 M5:933191e84e50e31ea6943a88e8bc6f61 SP:Mus musculus 37@RG ID:00001.3 PL:illumina PU:00001ABXX101026.3.TTGAGCCT LB:Solexa-45924 DT:2010-10-26T00:00:00-0400 SM:stat2_120 CN:BI 38@PG ID:00001ABXX.3 VN:0.7.1-9 CL:/seq/software/picard/current/3rd_party/maq/maq map 3900001ABXX101026:3:1:6530:123586 65 chrX 113054885 64 68M = 113054885 1 AGCCCTTTTTAAATACTGTAGATCACAAAGCAAAAAATAAAACTAAACATTAGGAAAAGAAAATGATA HHHHHHHHHHHHEHHHFCDC>B?EEEHE@HF;EEE@D@D@<9DEEB>E<FBD;@@<;C(?55?<B;6? MC:Z:68M PG:Z:00001ABXX.3 RG:Z:00001.3 NM:i:0 MQ:i:10 UQ:i:0 DS:i:136 4000001ABXX101026:3:1:6530:123586 129 chrX 113054885 10 68M = 113054885 -1 AGCCCTTTTTTTTTACTGTAGATCACAAAGGTAATTCTATAGTGTCTTTTCAGGATTCAAAGTCTTAG HHHHHGHGHHHFEHHHBEFEHEBCDEHEEBB5E=EHBHF=FF:FECF;BA?B@GCCGGGFFGCGF6EE MC:Z:68M PG:Z:00001ABXX.3 RG:Z:00001.3 NM:i:29 MQ:i:64 UQ:i:984 DS:i:136 4100001ABXX101026:3:1:6533:123569 1089 chrX 113054885 67 68M = 113054885 1 AGCCCTTTTTAAATACTGTAGATCACAAAGCAAAAAATAAAACTAAACATTAGGAAAAGAAAATGATA /HFHHHHFEFFHHHHHHHHHHHDHHHHHHHHHEHHHGHHHGHHFG?DHHHFHHFD@FFG?@EG@BHFG MC:Z:68M PG:Z:00001ABXX.3 RG:Z:00001.3 NM:i:0 MQ:i:10 UQ:i:0 DS:i:136 4200001ABXX101026:3:1:6533:123569 1153 chrX 113054885 10 68M = 113054885 -1 AGCCCTTTTTTTTTACTGTAGATCACAAAGGTAATTCTATAGTGTCTTTTCAGGATTCAAAGTCTTAG HHHHHHEHHHHHHG@=FGDBFDFDFFHFHFGCBC;DFCCEFD1C+D<D<?EB8FDEFCG.FGCFEB=D MC:Z:68M PG:Z:00001ABXX.3 RG:Z:00001.3 NM:i:29 MQ:i:67 UQ:i:964 DS:i:136 43