BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013333.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,482,282 number of mapped reads = 1,008,822 (68.06%) number of supplementary alignments = 12,699 (0.86%) number of secondary alignments = 0 number of mapped bases = 62,249,013 bp number of sequenced bases = 62,213,142 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 156,214 duplication rate = 11.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6887 >>>>>>> ACTG content number of A's = 16,190,576 bp (26.02%) number of C's = 11,650,736 bp (18.73%) number of T's = 19,510,821 bp (31.36%) number of G's = 14,854,135 bp (23.88%) number of N's = 6,874 bp (0.01%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 555,842 number of insertions = 4,622 mapped reads with insertion percentage = 0.45% number of deletions = 20,544 mapped reads with deletion percentage = 2% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2768X There is a 1.11% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.21% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% of reference with a coverageData >= 10X There is a 0% 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 5302780 0.021274891828654663 0.3497402077867886 chr2 243199373 5171957 0.02126632538645566 0.3656707274248185 chr3 198022430 5472578 0.027636152126807048 0.28128688401170115 chr4 191154276 4453175 0.023296235340296546 0.2700778511049509 chr5 180915260 2548041 0.014084168466496414 0.19129753837600294 chr6 171115067 3343148 0.019537426239619213 0.25505644037399633 chr7 159138663 3934576 0.024724199172139583 0.30849562705001055 chr8 146364022 3340804 0.022825308804372703 0.27913206661537426 chr9 141213431 2698636 0.019110335191841632 0.24110029991812573 chr10 135534747 2801892 0.020672868485894617 0.3566506521900802 chr11 135006516 2688136 0.019911157473317807 0.2468626748947471 chr12 133851895 2607977 0.01948404988961867 0.23123581200980486 chr13 115169878 1218659 0.010581403932719283 0.16717043073125135 chr14 107349540 1631079 0.015194093984939292 0.20459840720243103 chr15 102531392 1636754 0.01596344268884987 0.20655749295789227 chr16 90354753 1898369 0.02101017308962153 0.2507154881477564 chr17 81195210 1990109 0.024510177386079794 0.26931295560604546 chr18 78077248 1557037 0.019942262821558466 0.3018035095987575 chr19 59128983 1536677 0.025988557929366045 0.3223848546511456 chr20 63025520 1056328 0.016760321850577353 0.21275025096489802 chr21 48129895 942854 0.019589778868206547 0.25112432349890834 chr22 51304566 725813 0.014147142381050451 0.19255211798636362 chrMT 16571 213747 12.898859453261723 10.309703793649954 chrX 155270560 3243742 0.020890901662233972 0.2406781669335817 chrY 59373566 234145 0.003943589980766862 0.14302043499849493