BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472840.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,455,571 number of mapped reads = 2,154,684 (87.75%) number of supplementary alignments = 26,050 (1.06%) number of secondary alignments = 0 number of mapped bases = 139,324,796 bp number of sequenced bases = 139,272,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,115 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5005 >>>>>>> ACTG content number of A's = 37,464,969 bp (26.9%) number of C's = 28,448,189 bp (20.43%) number of T's = 40,605,131 bp (29.16%) number of G's = 32,750,370 bp (23.52%) number of N's = 3,454 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,153,574 number of insertions = 10,738 mapped reads with insertion percentage = 0.49% number of deletions = 29,457 mapped reads with deletion percentage = 1.35% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.3437X There is a 3.96% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 10271644 0.041210103945939616 0.4433408386472223 chr2 243199373 13603161 0.05593419436981854 0.5293610057553466 chr3 198022430 10747065 0.05427195797970967 0.2567564732790678 chr4 191154276 5768715 0.030178320468227455 0.23760639288017177 chr5 180915260 7123618 0.03937544019227565 0.21966886226056567 chr6 171115067 8644193 0.0505168431485931 0.2612912340208537 chr7 159138663 8533523 0.05362319149306916 0.4186962927519877 chr8 146364022 7596621 0.051902242751979036 0.324134894717607 chr9 141213431 8218124 0.05819647565959926 0.4076749526675735 chr10 135534747 5813886 0.04289590771877857 0.3462856388515397 chr11 135006516 4623652 0.03424762105556446 0.3122264117311804 chr12 133851895 5697786 0.042567839626028454 0.2385742680816292 chr13 115169878 5669589 0.04922805423133295 0.25258762495518106 chr14 107349540 2780495 0.025901321980513377 0.21798166683788164 chr15 102531392 2577565 0.025139276369133854 0.19138677131395318 chr16 90354753 4839923 0.053565781979394045 0.28878612430712314 chr17 81195210 3236133 0.03985620580327337 0.23846882057362298 chr18 78077248 2326016 0.029791213952622922 0.6743660341850855 chr19 59128983 3435172 0.05809624697925212 0.3783436860745652 chr20 63025520 6329653 0.10043000041887794 0.36802533540411364 chr21 48129895 2047548 0.04254212480621452 0.2695952254503104 chr22 51304566 1700808 0.03315120139599271 0.21633778351223 chrMT 16571 24052 1.4514513306378614 1.5587233354104049 chrX 155270560 6930970 0.04463801766413414 0.26449733423662997 chrY 59373566 784884 0.013219418217191132 0.19537520085664226