BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549156.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 = 12,826,774 number of mapped reads = 10,910,398 (85.06%) number of secondary alignments = 0 number of mapped bases = 432,297,891 bp number of sequenced bases = 432,253,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 942,784 duplication rate = 7.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7275 >>>>>>> ACTG content number of A's = 125,674,370 bp (29.07%) number of C's = 88,825,033 bp (20.55%) number of T's = 127,975,867 bp (29.61%) number of G's = 89,691,748 bp (20.75%) number of N's = 86,343 bp (0.02%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,405,488 number of insertions = 11,555 mapped reads with insertion percentage = 0.11% number of deletions = 35,211 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.21% >>>>>>> Coverage mean coverageData = 0.1396X std coverageData = 1.236X There is a 7.96% of reference with a coverageData >= 1X There is a 3.21% of reference with a coverageData >= 2X There is a 1.4% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 35565794 0.14269089423853432 1.5822252937718055 chr2 243199373 37002413 0.1521484720275163 0.8824760244179789 chr3 198022430 29775198 0.1503627543607055 0.6146723745335246 chr4 191154276 28165900 0.1473464292266211 0.734894754245477 chr5 180915260 26573369 0.1468829605639679 0.6276830757359704 chr6 171115067 25404661 0.14846536570622387 0.6440474801879652 chr7 159138663 24254134 0.1524088084113161 1.1848197370899947 chr8 146364022 22538250 0.15398763775431096 4.037089819832603 chr9 141213431 18253898 0.12926460231675838 0.7540289097976987 chr10 135534747 20915028 0.15431487838317948 1.0000028643953585 chr11 135006516 19891487 0.14733723667085816 0.8087645652492276 chr12 133851895 20100006 0.15016601744786653 0.6281621988510387 chr13 115169878 13681192 0.11879140828819841 0.5598162522231189 chr14 107349540 13387177 0.12470642165769877 0.6873842493648357 chr15 102531392 12949881 0.1263016208733419 0.5509903533309582 chr16 90354753 12512864 0.13848595214465365 0.6425478205703713 chr17 81195210 11870236 0.14619379640744817 0.6549370084012538 chr18 78077248 11218924 0.14369005423961664 1.469564758487683 chr19 59128983 8914016 0.1507554425551341 1.2743895834988181 chr20 63025520 9350027 0.14835303223202284 0.6617985046486583 chr21 48129895 5728623 0.1190242156148481 0.6994750008350762 chr22 51304566 5244289 0.102218757683283 0.513733385619115 chrMT 16571 368882 22.260696397320622 26.1821450230319 chrX 155270560 14519442 0.09351059209163669 0.5724488967894905 chrY 59373566 4112200 0.06925977799615404 0.8078072471713605