BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514703.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 109,525,720 number of mapped reads = 108,877,240 (99.41%) number of supplementary alignments = 4,379,519 (4%) number of secondary alignments = 0 number of mapped bases = 10,475,169,630 bp number of sequenced bases = 10,469,921,185 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,764,321 duplication rate = 49.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7997 >>>>>>> ACTG content number of A's = 2,999,627,879 bp (28.65%) number of C's = 2,232,907,705 bp (21.33%) number of T's = 2,970,933,159 bp (28.38%) number of G's = 2,260,936,372 bp (21.59%) number of N's = 5,516,070 bp (0.05%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 65,496,058 number of insertions = 2,817,482 mapped reads with insertion percentage = 2.52% number of deletions = 2,824,636 mapped reads with deletion percentage = 2.52% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 3.3838X std coverageData = 54.7963X There is a 7.21% of reference with a coverageData >= 1X There is a 5.11% of reference with a coverageData >= 2X There is a 4.4% of reference with a coverageData >= 3X There is a 4.02% of reference with a coverageData >= 4X There is a 3.76% of reference with a coverageData >= 5X There is a 3.57% of reference with a coverageData >= 6X There is a 3.42% of reference with a coverageData >= 7X There is a 3.29% of reference with a coverageData >= 8X There is a 3.17% of reference with a coverageData >= 9X There is a 3.07% of reference with a coverageData >= 10X There is a 2.98% of reference with a coverageData >= 11X There is a 2.89% of reference with a coverageData >= 12X There is a 2.82% of reference with a coverageData >= 13X There is a 2.75% of reference with a coverageData >= 14X There is a 2.68% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.56% of reference with a coverageData >= 17X There is a 2.5% of reference with a coverageData >= 18X There is a 2.45% of reference with a coverageData >= 19X There is a 2.4% of reference with a coverageData >= 20X There is a 2.35% of reference with a coverageData >= 21X There is a 2.3% of reference with a coverageData >= 22X There is a 2.26% of reference with a coverageData >= 23X There is a 2.21% of reference with a coverageData >= 24X There is a 2.17% of reference with a coverageData >= 25X There is a 2.13% of reference with a coverageData >= 26X There is a 2.1% of reference with a coverageData >= 27X There is a 2.06% of reference with a coverageData >= 28X There is a 2.02% of reference with a coverageData >= 29X There is a 1.99% of reference with a coverageData >= 30X There is a 1.96% of reference with a coverageData >= 31X There is a 1.93% of reference with a coverageData >= 32X There is a 1.89% of reference with a coverageData >= 33X There is a 1.86% of reference with a coverageData >= 34X There is a 1.84% of reference with a coverageData >= 35X There is a 1.81% of reference with a coverageData >= 36X There is a 1.78% of reference with a coverageData >= 37X There is a 1.75% of reference with a coverageData >= 38X There is a 1.73% of reference with a coverageData >= 39X There is a 1.7% of reference with a coverageData >= 40X There is a 1.68% of reference with a coverageData >= 41X There is a 1.65% of reference with a coverageData >= 42X There is a 1.63% of reference with a coverageData >= 43X There is a 1.61% of reference with a coverageData >= 44X There is a 1.59% of reference with a coverageData >= 45X There is a 1.56% of reference with a coverageData >= 46X There is a 1.54% of reference with a coverageData >= 47X There is a 1.52% of reference with a coverageData >= 48X There is a 1.5% of reference with a coverageData >= 49X There is a 1.48% of reference with a coverageData >= 50X There is a 1.46% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 811315525 3.2550190717478693 40.897047400574685 chr2 243199373 1658089653 6.817820426699867 97.89181100154008 chr3 198022430 712260877 3.5968696929938693 46.319436395990095 chr4 191154276 680634480 3.5606552688363613 37.902543578625256 chr5 180915260 411746105 2.2759058854405096 28.060128101244192 chr6 171115067 640212920 3.741417580720697 40.429993041217955 chr7 159138663 438523323 2.755605173081038 35.838184020809095 chr8 146364022 458014793 3.129285371783511 35.45812901115348 chr9 141213431 359808062 2.547973372306208 34.27593084555164 chr10 135534747 626018119 4.618875475526582 42.15124374183594 chr11 135006516 542152678 4.015751936002852 37.521595187262655 chr12 133851895 350727613 2.6202663249556535 31.380292302057555 chr13 115169878 214817238 1.865220678622235 24.076178055170462 chr14 107349540 454366786 4.23259183038884 125.0601149858782 chr15 102531392 345920340 3.373799314067637 47.197603166824265 chr16 90354753 180289506 1.9953516557120132 110.90827034835397 chr17 81195210 350445772 4.316089237283825 54.902375170452935 chr18 78077248 327128038 4.189799799296205 41.264307525970544 chr19 59128983 115107520 1.946719090365549 71.86543659713448 chr20 63025520 224462075 3.561447410509267 41.196144371674144 chr21 48129895 120032019 2.4939181562727284 30.456403343270434 chr22 51304566 99659847 1.9425141809015596 32.97470488001158 chrMT 16571 9663714 583.1702371613059 292.8457571038768 chrX 155270560 302065847 1.9454160981965931 44.61991284922448 chrY 59373566 41706780 0.7024469441501964 14.086870588504363