BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234126.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 = 5,035,923 number of mapped reads = 4,713,626 (93.6%) number of supplementary alignments = 33,358 (0.66%) number of secondary alignments = 0 number of mapped bases = 323,853,543 bp number of sequenced bases = 323,738,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 691,730 duplication rate = 5.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0161 >>>>>>> ACTG content number of A's = 82,555,486 bp (25.5%) number of C's = 59,442,984 bp (18.36%) number of T's = 90,020,461 bp (27.81%) number of G's = 91,649,309 bp (28.31%) number of N's = 70,619 bp (0.02%) GC percentage = 46.67% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 2,189,273 number of insertions = 23,648 mapped reads with insertion percentage = 0.5% number of deletions = 68,256 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.1046X std coverageData = 48.4394X There is a 5.62% of reference with a coverageData >= 1X There is a 2.08% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.1% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 8688061 0.034856727598684696 2.4014018844018583 chr2 243199373 31365864 0.1289718127686127 172.7498123163663 chr3 198022430 18321624 0.0925229732813601 0.46583643579495465 chr4 191154276 16280979 0.08517193201579232 0.5029863781749245 chr5 180915260 11678722 0.06455354844030294 0.47021342967856544 chr6 171115067 9194724 0.05373415772907946 0.4244316703328639 chr7 159138663 44954085 0.28248374186730474 4.214228062102046 chr8 146364022 23006041 0.15718371691097693 0.9205763874052995 chr9 141213431 9535803 0.0675275923293727 1.1532265677520195 chr10 135534747 1814549 0.013388072359038675 0.30074618602609976 chr11 135006516 20937604 0.1550858774846097 1.3137651691424055 chr12 133851895 10476853 0.07827198113257941 0.44355309374855256 chr13 115169878 5483974 0.047616391501256954 0.32762851274562976 chr14 107349540 35124504 0.3271975268827421 1.0238145080046355 chr15 102531392 6609422 0.06446242337176111 0.39459058226272853 chr16 90354753 1563288 0.01730166867923373 0.5107864981736874 chr17 81195210 6849684 0.08436069073532786 0.6917132830842294 chr18 78077248 5131222 0.06571981123105158 2.51306913953885 chr19 59128983 16841379 0.28482443203868396 1.258405662504117 chr20 63025520 21213718 0.33658933714469946 0.9499560436942581 chr21 48129895 9484668 0.19706396616905147 0.7838776203868412 chr22 51304566 6735528 0.1312851569585444 0.5741895066522983 chrMT 16571 27730 1.6734053466900005 1.8631323420051424 chrX 155270560 1761716 0.011346104503004304 0.5228771317302747 chrY 59373566 771801 0.012999067632218688 0.34619928400191247