BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549142.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 = 13,014,358 number of mapped reads = 11,417,239 (87.73%) number of secondary alignments = 0 number of mapped bases = 453,306,128 bp number of sequenced bases = 453,263,007 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 604,890 duplication rate = 4.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5109 >>>>>>> ACTG content number of A's = 131,204,327 bp (28.95%) number of C's = 94,464,648 bp (20.84%) number of T's = 132,922,710 bp (29.33%) number of G's = 94,567,939 bp (20.86%) number of N's = 103,383 bp (0.02%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,448,789 number of insertions = 11,273 mapped reads with insertion percentage = 0.1% number of deletions = 34,243 mapped reads with deletion percentage = 0.3% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.1464X std coverageData = 0.8073X There is a 10.29% of reference with a coverageData >= 1X There is a 2.87% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 37223498 0.1493416459732712 1.5230738473683711 chr2 243199373 38132138 0.15679373482595285 0.7625675771978474 chr3 198022430 31800445 0.1605901159782758 0.5332455349320975 chr4 191154276 29993941 0.15690960007611862 0.5638107417442427 chr5 180915260 28411687 0.15704417084551076 0.5370099722366979 chr6 171115067 26261878 0.15347495963052746 0.5918238385420048 chr7 159138663 25386381 0.15952365390929543 1.1686086367188693 chr8 146364022 23350245 0.15953541506258964 0.7507189576037543 chr9 141213431 19762651 0.13994880557784903 0.7288723155961122 chr10 135534747 21912935 0.16167761762229135 0.7670275817796274 chr11 135006516 21611003 0.1600737774760442 0.7328267422501685 chr12 133851895 20327612 0.15186644910779934 0.5433289600446467 chr13 115169878 14478642 0.12571552780493525 0.4633361393412326 chr14 107349540 14307605 0.1332805431676745 0.6167093107282555 chr15 102531392 13779268 0.13439072396481264 0.48270986453194614 chr16 90354753 13143434 0.1454647770438817 0.5633823511726687 chr17 81195210 12569114 0.1548011760792293 0.5692693697935457 chr18 78077248 12054961 0.15439787273239958 1.4153929709744513 chr19 59128983 8994064 0.15210922873474755 1.2818812136127347 chr20 63025520 9865525 0.15653222694552937 0.567378214980639 chr21 48129895 6003837 0.12474236646475127 0.5631024816148108 chr22 51304566 5386982 0.10500005009300732 0.4593326805474662 chrMT 16571 7159 0.43201979361535214 0.8748275103485793 chrX 155270560 14741818 0.09494277601626477 0.515077864634766 chrY 59373566 3799305 0.06398984019251934 0.5040128133009347