BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236092.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 = 1,281,582 number of mapped reads = 1,104,939 (86.22%) number of supplementary alignments = 7,916 (0.62%) number of secondary alignments = 0 number of mapped bases = 72,695,975 bp number of sequenced bases = 72,657,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,721 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4492 >>>>>>> ACTG content number of A's = 20,065,877 bp (27.62%) number of C's = 12,775,711 bp (17.58%) number of T's = 23,713,997 bp (32.64%) number of G's = 16,061,875 bp (22.11%) number of N's = 39,827 bp (0.05%) GC percentage = 39.69% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 587,129 number of insertions = 5,145 mapped reads with insertion percentage = 0.46% number of deletions = 22,619 mapped reads with deletion percentage = 2.02% homopolymer indels = 46.65% >>>>>>> Coverage mean coverageData = 0.0235X std coverageData = 0.2477X There is a 1.97% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5460903 0.02190928543363589 0.3906365228115831 chr2 243199373 5945784 0.024448188030484767 0.261324520252012 chr3 198022430 6731426 0.03399325015858052 0.21223295355986793 chr4 191154276 2556351 0.013373234716444428 0.13770045738927358 chr5 180915260 3094218 0.0171031343624634 0.15031474869170613 chr6 171115067 8168907 0.0477392619084794 0.3264468763421668 chr7 159138663 3331564 0.02093497543082915 0.2740862274949711 chr8 146364022 5733579 0.039173417904572204 0.449021018812722 chr9 141213431 2439155 0.017272825840482554 0.18247823859421147 chr10 135534747 4616026 0.03405787889949726 0.262521466186017 chr11 135006516 2334201 0.017289543269155987 0.16609346237606773 chr12 133851895 3454584 0.025809003301746306 0.187048602649541 chr13 115169878 2672421 0.0232041662838264 0.175989635692485 chr14 107349540 2203552 0.020526888145026054 0.16603019843877628 chr15 102531392 1524699 0.014870557887285876 0.142301623800057 chr16 90354753 1838999 0.020353096422055406 0.17031511837115232 chr17 81195210 2143529 0.02639969771615838 0.18623439058513086 chr18 78077248 1150327 0.014733190903449876 0.29898345542554566 chr19 59128983 806733 0.013643613657282082 0.2574682239528236 chr20 63025520 945996 0.015009729392157336 0.14167236692956606 chr21 48129895 2000485 0.041564291798268 0.23812801408667197 chr22 51304566 1060400 0.02066872566469035 0.16391740458296583 chrMT 16571 167235 10.09202824210971 6.851544448626868 chrX 155270560 2171491 0.013985207498446582 0.1424305967393152 chrY 59373566 143410 0.002415384651142564 0.06484355673227378