BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163152.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 149,748,722 number of mapped reads = 148,335,243 (99.06%) number of supplementary alignments = 781,730 (0.52%) number of secondary alignments = 0 number of mapped bases = 14,637,139,051 bp number of sequenced bases = 14,635,403,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,516,128 duplication rate = 48.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3193 >>>>>>> ACTG content number of A's = 3,583,294,733 bp (24.48%) number of C's = 3,735,880,544 bp (25.53%) number of T's = 3,588,681,332 bp (24.52%) number of G's = 3,727,067,199 bp (25.47%) number of N's = 479,682 bp (0%) GC percentage = 50.99% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 45,089,076 number of insertions = 1,047,951 mapped reads with insertion percentage = 0.7% number of deletions = 734,109 mapped reads with deletion percentage = 0.49% homopolymer indels = 45.53% >>>>>>> Coverage mean coverageData = 4.7282X std coverageData = 59.177X There is a 15.41% of reference with a coverageData >= 1X There is a 9.25% of reference with a coverageData >= 2X There is a 6.4% of reference with a coverageData >= 3X There is a 5.46% of reference with a coverageData >= 4X There is a 4.86% of reference with a coverageData >= 5X There is a 4.51% of reference with a coverageData >= 6X There is a 4.24% of reference with a coverageData >= 7X There is a 4.03% of reference with a coverageData >= 8X There is a 3.86% of reference with a coverageData >= 9X There is a 3.71% of reference with a coverageData >= 10X There is a 3.58% of reference with a coverageData >= 11X There is a 3.46% of reference with a coverageData >= 12X There is a 3.36% of reference with a coverageData >= 13X There is a 3.26% of reference with a coverageData >= 14X There is a 3.17% of reference with a coverageData >= 15X There is a 3.09% of reference with a coverageData >= 16X There is a 3.02% of reference with a coverageData >= 17X There is a 2.95% of reference with a coverageData >= 18X There is a 2.88% of reference with a coverageData >= 19X There is a 2.82% of reference with a coverageData >= 20X There is a 2.76% of reference with a coverageData >= 21X There is a 2.7% of reference with a coverageData >= 22X There is a 2.65% of reference with a coverageData >= 23X There is a 2.6% of reference with a coverageData >= 24X There is a 2.55% of reference with a coverageData >= 25X There is a 2.5% of reference with a coverageData >= 26X There is a 2.45% of reference with a coverageData >= 27X There is a 2.41% of reference with a coverageData >= 28X There is a 2.37% of reference with a coverageData >= 29X There is a 2.33% of reference with a coverageData >= 30X There is a 2.29% of reference with a coverageData >= 31X There is a 2.25% of reference with a coverageData >= 32X There is a 2.22% of reference with a coverageData >= 33X There is a 2.18% of reference with a coverageData >= 34X There is a 2.15% of reference with a coverageData >= 35X There is a 2.12% of reference with a coverageData >= 36X There is a 2.09% of reference with a coverageData >= 37X There is a 2.06% of reference with a coverageData >= 38X There is a 2.03% of reference with a coverageData >= 39X There is a 2% of reference with a coverageData >= 40X There is a 1.97% of reference with a coverageData >= 41X There is a 1.94% of reference with a coverageData >= 42X There is a 1.92% of reference with a coverageData >= 43X There is a 1.89% of reference with a coverageData >= 44X There is a 1.87% of reference with a coverageData >= 45X There is a 1.84% of reference with a coverageData >= 46X There is a 1.82% of reference with a coverageData >= 47X There is a 1.79% of reference with a coverageData >= 48X There is a 1.77% of reference with a coverageData >= 49X There is a 1.75% of reference with a coverageData >= 50X There is a 1.73% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1603859531 6.4347263190971145 66.02982342333938 chr2 243199373 972325427 3.9980589382522793 46.447991073592725 chr3 198022430 702186554 3.545995037026866 42.60207034160955 chr4 191154276 523561506 2.7389473934655797 38.4638351809559 chr5 180915260 729730998 4.0335513875391165 58.552996009123746 chr6 171115067 768175885 4.48923580177776 53.39703371627585 chr7 159138663 782591731 4.917671898500241 56.34076864838138 chr8 146364022 651880971 4.453833408595454 76.61396289575757 chr9 141213431 651936477 4.616674719843044 58.63915996990867 chr10 135534747 592135170 4.368880918780185 49.9856693541848 chr11 135006516 743657393 5.50830741384364 56.999645331723585 chr12 133851895 684284215 5.112248989825658 55.2870679617236 chr13 115169878 273784931 2.377226890871587 33.86908480773702 chr14 107349540 427312429 3.980570657312551 45.69409363740546 chr15 102531392 599765632 5.84958050701194 58.23206010408626 chr16 90354753 535695697 5.928804841069069 53.25406435710446 chr17 81195210 720166759 8.869571973519127 76.8875860291894 chr18 78077248 221656469 2.838938034803686 38.11420660709313 chr19 59128983 789574811 13.35343127751749 95.19520050859397 chr20 63025520 334562104 5.308359280494631 57.629340010457376 chr21 48129895 219886465 4.568604710232591 166.08036870330528 chr22 51304566 304723550 5.939501564051823 61.057300917722195 chrMT 16571 3620 0.21845392553255688 0.5891213410435949 chrX 155270560 789041223 5.081718150562477 62.28898166866822 chrY 59373566 14639503 0.24656600548466298 14.455450780271267