BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971321.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 55,367,004 number of mapped reads = 48,566,494 (87.72%) number of secondary alignments = 0 number of mapped bases = 1,919,945,209 bp number of sequenced bases = 1,919,734,506 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,481,415 duplication rate = 12.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.7565 >>>>>>> ACTG content number of A's = 562,852,166 bp (29.32%) number of C's = 398,705,729 bp (20.77%) number of T's = 560,259,610 bp (29.18%) number of G's = 397,878,073 bp (20.73%) number of N's = 38,928 bp (0%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 6,184,510 number of insertions = 69,503 mapped reads with insertion percentage = 0.14% number of deletions = 161,214 mapped reads with deletion percentage = 0.33% homopolymer indels = 39.24% >>>>>>> Coverage mean coverageData = 0.6202X std coverageData = 7.508X There is a 27.15% of reference with a coverageData >= 1X There is a 14.41% of reference with a coverageData >= 2X There is a 7.84% of reference with a coverageData >= 3X There is a 4.37% of reference with a coverageData >= 4X There is a 2.5% of reference with a coverageData >= 5X There is a 1.47% of reference with a coverageData >= 6X There is a 0.9% of reference with a coverageData >= 7X There is a 0.57% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.18% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 147496373 0.5917592999698083 8.013364003778431 chr2 243199373 158432856 0.6514525676840458 4.406157873224221 chr3 198022430 127682946 0.6447903199652686 1.538624640357687 chr4 191154276 126541062 0.6619839464119547 1.825274070079223 chr5 180915260 149970524 0.8289545282139273 1.9056568841513186 chr6 171115067 110738678 0.6471591306451114 2.080267450027034 chr7 159138663 106450319 0.6689155042103125 7.01973035850498 chr8 146364022 98803293 0.6750517760437056 28.745789340198964 chr9 141213431 79229866 0.5610646624682606 4.552697302896862 chr10 135534747 86570477 0.6387327155301363 3.6317547746743326 chr11 135006516 85723057 0.6349549602479928 4.331317757450634 chr12 133851895 86170011 0.6437713190388527 1.865037419215702 chr13 115169878 60819331 0.5280836626396357 1.3052605188081279 chr14 107349540 57365077 0.5343765515902537 2.6105115739598808 chr15 102531392 52683367 0.5138267019724067 1.3773805302354003 chr16 90354753 50603847 0.5600573884585794 2.194824552466591 chr17 81195210 47762920 0.5882480013291425 1.936404319227504 chr18 78077248 49907957 0.6392125526760369 9.291006837000506 chr19 59128983 38209698 0.6462092879223037 8.282354900115276 chr20 63025520 36276398 0.5755826846014123 1.8130649848626148 chr21 48129895 23498900 0.4882391702703694 2.196494776624184 chr22 51304566 19738020 0.38472248259540875 1.6313768196584746 chrMT 16571 62740 3.7861323999758616 4.4478218263569405 chrX 155270560 112127008 0.722139522134782 3.010885997731626 chrY 59373566 7080484 0.11925313699365808 1.3021705067447829