BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068939.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 = 1,927,458 number of mapped reads = 1,487,805 (77.19%) number of supplementary alignments = 6,323 (0.33%) number of secondary alignments = 0 number of mapped bases = 93,154,474 bp number of sequenced bases = 93,110,987 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,500 duplication rate = 3.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6883 >>>>>>> ACTG content number of A's = 23,499,563 bp (25.24%) number of C's = 15,922,863 bp (17.1%) number of T's = 30,588,455 bp (32.85%) number of G's = 22,890,581 bp (24.58%) number of N's = 209,525 bp (0.23%) GC percentage = 41.69% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 901,988 number of insertions = 8,116 mapped reads with insertion percentage = 0.54% number of deletions = 26,840 mapped reads with deletion percentage = 1.79% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.3439X There is a 2.67% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 8522789 0.03419365201902546 0.5931578974591585 chr2 243199373 7056117 0.029013713781244 0.30783191691158995 chr3 198022430 4615284 0.023306874882809994 0.16679195448534595 chr4 191154276 3255079 0.017028544001809302 0.1788647901548614 chr5 180915260 6033767 0.033351343606946145 0.20147754292204884 chr6 171115067 5640640 0.032964017131232516 0.2535076903433218 chr7 159138663 5913541 0.03715967501876021 0.6458917478163061 chr8 146364022 4824794 0.03296434420201981 0.4490424086108524 chr9 141213431 4283616 0.03033433838173651 0.282309518153965 chr10 135534747 5737307 0.04233089393674081 0.3187151682404686 chr11 135006516 4756341 0.03523045509892278 0.4085247366084537 chr12 133851895 3077578 0.022992412621427587 0.16984651478126037 chr13 115169878 2341707 0.020332634197980134 0.15558132410653164 chr14 107349540 3792570 0.035329168620564184 0.21236095570305583 chr15 102531392 2659743 0.025940767487093123 0.1755732701462091 chr16 90354753 2737407 0.030296214743678176 0.2097480955110717 chr17 81195210 2542267 0.031310553910754095 0.23034062369557956 chr18 78077248 1934912 0.024782021005658395 0.5578329302628086 chr19 59128983 1472181 0.024897789972136 0.4571583220331192 chr20 63025520 1903970 0.03020950878310881 0.20096820639070928 chr21 48129895 1774504 0.03686906027947911 0.2244932693243679 chr22 51304566 1213333 0.02364961044597863 0.16527926919064112 chrMT 16571 150438 9.078389958360992 5.451628325065438 chrX 155270560 6612574 0.04258742932336948 0.2877980297567143 chrY 59373566 302015 0.005086691272678485 0.13465982283433994