BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971285.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 = 11,545,241 number of mapped reads = 9,708,448 (84.09%) number of secondary alignments = 0 number of mapped bases = 382,663,860 bp number of sequenced bases = 382,624,846 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 735,551 duplication rate = 6.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.2802 >>>>>>> ACTG content number of A's = 110,781,466 bp (28.95%) number of C's = 77,714,669 bp (20.31%) number of T's = 114,220,826 bp (29.85%) number of G's = 79,905,083 bp (20.88%) number of N's = 2,802 bp (0%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,163,845 number of insertions = 13,885 mapped reads with insertion percentage = 0.14% number of deletions = 31,044 mapped reads with deletion percentage = 0.32% homopolymer indels = 40.32% >>>>>>> Coverage mean coverageData = 0.1236X std coverageData = 1.2352X There is a 9.58% of reference with a coverageData >= 1X There is a 1.92% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 30580913 0.12269142149900601 2.2350034308385 chr2 243199373 32765273 0.13472597645225015 0.8927432928557413 chr3 198022430 26359044 0.13311140561198043 0.45455608747181747 chr4 191154276 26093450 0.13650466286194926 0.4840926277704794 chr5 180915260 24134211 0.13340063740338987 0.4849902227211492 chr6 171115067 22704273 0.13268424223566472 0.5145495375157156 chr7 159138663 21722495 0.13650042416153765 1.638751616508191 chr8 146364022 20186782 0.13792174964965093 3.2792728574143584 chr9 141213431 16159899 0.11443599157363438 0.9071424995357129 chr10 135534747 17954096 0.13246858386801724 0.8250042592040137 chr11 135006516 17620036 0.13051248578253807 0.786828564133189 chr12 133851895 17605657 0.13153087597302973 0.4990610982581449 chr13 115169878 9155517 0.0794957601674285 0.3365059239686116 chr14 107349540 11818471 0.11009335484809717 0.6544733166146214 chr15 102531392 10486088 0.10227197539656928 0.38840957250007113 chr16 90354753 10040742 0.11112577553059107 0.5004103417606854 chr17 81195210 9346452 0.115110879077719 0.5176672487183084 chr18 78077248 10409557 0.13332382053219907 1.9476315988751327 chr19 59128983 7088624 0.11988408459519759 2.075755559382533 chr20 63025520 7361364 0.11679973445677243 0.47803077747340805 chr21 48129895 4858792 0.10095164346400506 0.5116658850856899 chr22 51304566 3820016 0.07445762234885682 0.33184729570837285 chrMT 16571 40207 2.426347233118098 2.8959633975318586 chrX 155270560 22995252 0.14809795237422987 0.6975131233031167 chrY 59373566 1356649 0.022849377111693107 0.2805624540824963