BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038480.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 17,627,970 number of mapped reads = 16,452,679 (93.33%) number of supplementary alignments = 240,125 (1.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,344,842 number of mapped paired reads (second in pair) = 8,107,837 number of mapped paired reads (both in pair) = 16,172,278 number of mapped paired reads (singletons) = 280,401 number of mapped bases = 2,219,519,105 bp number of sequenced bases = 2,217,980,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,274,057 duplication rate = 14.1% >>>>>>> Insert size mean insert size = 75,615.9144 std insert size = 2,655,520.4131 median insert size = 256 >>>>>>> Mapping quality mean mapping quality = 53.3781 >>>>>>> ACTG content number of A's = 634,922,568 bp (28.63%) number of C's = 437,883,853 bp (19.74%) number of T's = 647,450,002 bp (29.19%) number of G's = 497,546,774 bp (22.43%) number of N's = 176,807 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 27,698,889 number of insertions = 396,798 mapped reads with insertion percentage = 2.29% number of deletions = 797,562 mapped reads with deletion percentage = 4.68% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.717X std coverageData = 8.8138X There is a 26.9% of reference with a coverageData >= 1X There is a 15.62% of reference with a coverageData >= 2X There is a 9.03% of reference with a coverageData >= 3X There is a 5.64% of reference with a coverageData >= 4X There is a 3.53% of reference with a coverageData >= 5X There is a 2.29% of reference with a coverageData >= 6X There is a 1.5% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.69% of reference with a coverageData >= 9X There is a 0.48% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.25% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 194520995 0.7804233113625824 12.69176886274422 chr2 243199373 201296112 0.8276999628613352 10.488945378566456 chr3 198022430 177873115 0.8982473096608299 1.9244424403515423 chr4 191154276 95959772 0.5020017025410407 9.24973670445982 chr5 180915260 155226687 0.8580077048226888 1.8083222821915665 chr6 171115067 131569151 0.7688928468233601 7.578264398013449 chr7 159138663 108487659 0.6817177985214065 9.073422182406675 chr8 146364022 141293822 0.9653589732591524 3.708158491561035 chr9 141213431 95457734 0.6759819751139677 15.438596883970463 chr10 135534747 116108505 0.8566696553467577 19.91952886614387 chr11 135006516 103795873 0.7688212100814452 7.247060124490471 chr12 133851895 92759497 0.6930009993508123 1.7379166259408452 chr13 115169878 74425649 0.6462249530211364 1.515336970248017 chr14 107349540 72926574 0.6793375546835133 1.652626428603787 chr15 102531392 36473378 0.35572888740260156 1.0964268188127804 chr16 90354753 67377564 0.7457002732329975 7.830482468274513 chr17 81195210 56371905 0.6942762387091553 11.558527290199548 chr18 78077248 88865804 1.1381779747155023 10.534647605491559 chr19 59128983 31773846 0.537365000849076 5.38185797448258 chr20 63025520 59151928 0.9385393091560371 3.30820310499717 chr21 48129895 21726160 0.4514067608084331 4.168654959354669 chr22 51304566 13059250 0.25454362093229677 0.949965377794838 chrMT 16571 4076090 245.977309758011 149.30205770685498 chrX 155270560 74618020 0.4805677264254087 2.0618015389924125 chrY 59373566 4324015 0.07282727468314772 9.052871401721198