BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818991.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,105,876 number of mapped reads = 1,982,414 (94.14%) number of supplementary alignments = 27,649 (1.31%) number of secondary alignments = 0 number of mapped bases = 183,497,192 bp number of sequenced bases = 183,387,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 854,456 duplication rate = 36.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2172 >>>>>>> ACTG content number of A's = 53,531,889 bp (29.19%) number of C's = 38,453,371 bp (20.97%) number of T's = 52,532,208 bp (28.65%) number of G's = 38,860,963 bp (21.19%) number of N's = 8,909 bp (0%) GC percentage = 42.16% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,147,287 number of insertions = 27,885 mapped reads with insertion percentage = 1.37% number of deletions = 58,486 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.32% >>>>>>> Coverage mean coverageData = 0.0593X std coverageData = 0.6837X There is a 2.82% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 18241841 0.07318674243142607 1.2092097183381363 chr2 243199373 14796879 0.06084258695847871 0.9069534974266711 chr3 198022430 9936209 0.05017718952342924 0.40418410366846996 chr4 191154276 10472563 0.05478592066650918 0.5029369248581689 chr5 180915260 9742996 0.053853920338173794 0.4352585522945798 chr6 171115067 7799235 0.04557889107450719 0.45694383863176347 chr7 159138663 9149609 0.05749457000276545 0.8184352968787375 chr8 146364022 17142696 0.11712370134239683 0.684581417290323 chr9 141213431 7969121 0.05643316604919825 0.6191940659755459 chr10 135534747 9826976 0.07250521521245028 0.8324473623511677 chr11 135006516 6287492 0.04657176695086332 0.4642784797627575 chr12 133851895 7603670 0.05680659209195357 0.4374222256502542 chr13 115169878 4007606 0.03479734518777557 0.334169891265328 chr14 107349540 4286498 0.039930287544781284 0.38055032507854847 chr15 102531392 4657073 0.04542094776202785 0.3860352687954538 chr16 90354753 5868276 0.0649470648212607 0.7632251935702357 chr17 81195210 6490428 0.07993609475238748 0.5960169776856207 chr18 78077248 4275671 0.05476206077345349 0.7423255078144384 chr19 59128983 3815021 0.06452032161621991 1.1153479288533332 chr20 63025520 5328724 0.08454867171266496 0.5716101656022092 chr21 48129895 2560682 0.05320356506075902 0.47139199528400816 chr22 51304566 1500428 0.029245506140720495 0.3364548597517723 chrMT 16571 26605 1.6055156598877558 2.6435210633036235 chrX 155270560 11020231 0.07097437530978185 0.5588589620012304 chrY 59373566 690662 0.011632483048095848 0.6520160459217126