BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237810.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 = 4,152,867 number of mapped reads = 2,067,065 (49.77%) number of supplementary alignments = 21,553 (0.52%) number of secondary alignments = 0 number of mapped bases = 149,752,894 bp number of sequenced bases = 149,674,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,642 duplication rate = 8.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6844 >>>>>>> ACTG content number of A's = 45,379,458 bp (30.32%) number of C's = 28,875,697 bp (19.29%) number of T's = 45,487,294 bp (30.39%) number of G's = 29,674,688 bp (19.83%) number of N's = 257,725 bp (0.17%) GC percentage = 39.12% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,300,604 number of insertions = 11,651 mapped reads with insertion percentage = 0.56% number of deletions = 43,661 mapped reads with deletion percentage = 2.09% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.7824X There is a 1.25% of reference with a coverageData >= 1X There is a 0.72% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.34% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 6558236 0.02631181408370493 0.6915055884443745 chr2 243199373 7808039 0.03210550629174525 0.5846308190967112 chr3 198022430 9760571 0.04929022939472059 0.6497486658323679 chr4 191154276 21526427 0.1126128457623412 1.0278203437150133 chr5 180915260 4556259 0.025184492452433257 0.4482362008636768 chr6 171115067 10875212 0.06355496444974071 0.75028602521503 chr7 159138663 5301503 0.033313733445152795 0.5610820717381396 chr8 146364022 9562011 0.06533033780665033 1.7229469842235952 chr9 141213431 3316864 0.023488304026831556 0.571596300960419 chr10 135534747 4042403 0.029825584136000196 0.6037276600785891 chr11 135006516 13291299 0.09844931484640342 0.9894918626708562 chr12 133851895 15998472 0.11952368698254141 1.0575954379695622 chr13 115169878 3775789 0.0327845185353066 0.5305015297369078 chr14 107349540 2941927 0.02740511976110936 0.5193070514405189 chr15 102531392 2346370 0.022884405977829696 0.4302965498974779 chr16 90354753 2315827 0.02563038382717952 0.47216551692432807 chr17 81195210 2101514 0.02588224108294073 0.4539239018994189 chr18 78077248 4764658 0.06102492239480572 1.0725600513635087 chr19 59128983 1311928 0.022187562400658913 0.514282084621424 chr20 63025520 8466390 0.1343327274412016 1.1287882158445002 chr21 48129895 1684540 0.034999868584795375 0.5419637116117945 chr22 51304566 801156 0.015615686136005906 0.374257825352449 chrMT 16571 294242 17.75644197694768 14.947155835487672 chrX 155270560 5756623 0.03707478739047505 0.561603356992687 chrY 59373566 594634 0.010015130302262795 0.6767626203090106