BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971276.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 11,262,167 number of mapped reads = 8,274,120 (73.47%) number of secondary alignments = 0 number of mapped bases = 326,564,992 bp number of sequenced bases = 326,532,458 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 411,491 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2293 >>>>>>> ACTG content number of A's = 93,729,616 bp (28.7%) number of C's = 67,383,519 bp (20.64%) number of T's = 95,785,063 bp (29.33%) number of G's = 69,631,507 bp (21.32%) number of N's = 2,753 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0027 number of mismatches = 872,444 number of insertions = 10,568 mapped reads with insertion percentage = 0.13% number of deletions = 25,623 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.76% >>>>>>> Coverage mean coverageData = 0.1055X std coverageData = 0.714X There is a 8.41% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27192819 0.10909829989952162 0.998807018383259 chr2 243199373 27369118 0.11253778191278478 0.5470038705942974 chr3 198022430 23051516 0.11640861088312067 0.41096096058423065 chr4 191154276 19797583 0.10356861177408347 0.400421483630525 chr5 180915260 20682038 0.1143189247827961 0.4122568859760504 chr6 171115067 19135803 0.11183002955549204 0.48652349327103445 chr7 159138663 17453792 0.10967662836277567 0.7329199474423886 chr8 146364022 16647495 0.1137403493872285 2.0647585727363924 chr9 141213431 13599972 0.09630792130530416 0.5406878192290627 chr10 135534747 15424432 0.1138042630499764 0.5090465542992773 chr11 135006516 15569538 0.11532434478940261 0.6984602124619542 chr12 133851895 15287806 0.11421434115669413 0.4173201976328305 chr13 115169878 12110807 0.10515602873174877 0.3881785204427127 chr14 107349540 10213374 0.0951412926408441 0.40921748829919613 chr15 102531392 10139814 0.09889472679742806 0.3734553413022426 chr16 90354753 9146403 0.10122769081112977 0.4041971785901609 chr17 81195210 8823043 0.10866457516397827 0.4438212502711898 chr18 78077248 8354905 0.10700819014522643 0.911500483365999 chr19 59128983 5780295 0.09775738913013268 0.8778221161492266 chr20 63025520 7207207 0.11435378875096945 0.413797438095046 chr21 48129895 3718596 0.0772616686572867 0.3693532047757542 chr22 51304566 3595857 0.07008844008153192 0.31533140070716753 chrMT 16571 26257 1.5845151167702614 2.0401554892483995 chrX 155270560 15367808 0.09897438381107146 0.43457333389888053 chrY 59373566 868714 0.01463132600120397 0.22734907740370833