BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549059.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 = 8,490,603 number of mapped reads = 7,277,111 (85.71%) number of secondary alignments = 0 number of mapped bases = 289,383,512 bp number of sequenced bases = 289,355,694 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 307,722 duplication rate = 2.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9815 >>>>>>> ACTG content number of A's = 85,243,286 bp (29.46%) number of C's = 59,660,619 bp (20.62%) number of T's = 84,979,259 bp (29.37%) number of G's = 59,467,211 bp (20.55%) number of N's = 5,319 bp (0%) GC percentage = 41.17% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 875,691 number of insertions = 6,713 mapped reads with insertion percentage = 0.09% number of deletions = 22,074 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.78% >>>>>>> Coverage mean coverageData = 0.0935X std coverageData = 1.1229X There is a 7.41% of reference with a coverageData >= 1X There is a 1.39% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 23780523 0.09540807924406335 1.9198278491076923 chr2 243199373 24876972 0.10229044463860522 0.5491321924829101 chr3 198022430 19980309 0.10089922136598364 0.38339497318918486 chr4 191154276 19291410 0.10092063020342794 0.43808694718363034 chr5 180915260 18267408 0.10097217890851219 0.3935516429263722 chr6 171115067 17147160 0.10020835862455058 0.43100166207102286 chr7 159138663 16078536 0.10103475608564086 0.7711061621722887 chr8 146364022 15593855 0.1065415857457101 3.8887265640941266 chr9 141213431 12279168 0.08695467501246394 0.4889097020985182 chr10 135534747 13928095 0.10276401666946705 0.6332608250249013 chr11 135006516 13650005 0.10110626808560855 0.5441683481738256 chr12 133851895 13293821 0.09931739106121733 0.39403379973953495 chr13 115169878 9541386 0.08284619351598167 0.33998250431766897 chr14 107349540 9030468 0.08412209311749264 0.3893622209178985 chr15 102531392 8411054 0.08203393942023142 0.33823128825343535 chr16 90354753 8041350 0.08899753176238553 0.40585918164991475 chr17 81195210 7604956 0.093662618767782 0.40189857070348256 chr18 78077248 7860985 0.10068214750601866 1.01446562981669 chr19 59128983 5365061 0.09073487700608684 1.3312230557136995 chr20 63025520 6199204 0.09836021979667918 0.3968917953056524 chr21 48129895 3846144 0.07991174715839293 0.42423956993624323 chr22 51304566 3297579 0.06427457158491508 0.32832507396560023 chrMT 16571 7733 0.4666586204815642 0.9427626708841949 chrX 155270560 8967758 0.05775568787798537 0.36717112709136507 chrY 59373566 3042572 0.05124455553166539 0.6933622324988205