BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514751.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 = 69,133,902 number of mapped reads = 65,721,440 (95.06%) number of supplementary alignments = 10,239,711 (14.81%) number of secondary alignments = 0 number of mapped bases = 6,218,350,882 bp number of sequenced bases = 6,212,111,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,642,425 duplication rate = 44.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2518 >>>>>>> ACTG content number of A's = 1,905,557,181 bp (30.67%) number of C's = 1,186,383,125 bp (19.1%) number of T's = 1,884,800,404 bp (30.34%) number of G's = 1,234,945,319 bp (19.88%) number of N's = 425,218 bp (0.01%) GC percentage = 38.98% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 36,390,494 number of insertions = 4,760,095 mapped reads with insertion percentage = 6.86% number of deletions = 2,168,502 mapped reads with deletion percentage = 3.11% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 2.0087X std coverageData = 171.3396X There is a 5.97% of reference with a coverageData >= 1X There is a 4% of reference with a coverageData >= 2X There is a 3.27% of reference with a coverageData >= 3X There is a 2.85% of reference with a coverageData >= 4X There is a 2.58% of reference with a coverageData >= 5X There is a 2.37% of reference with a coverageData >= 6X There is a 2.2% of reference with a coverageData >= 7X There is a 2.07% of reference with a coverageData >= 8X There is a 1.95% of reference with a coverageData >= 9X There is a 1.85% of reference with a coverageData >= 10X There is a 1.77% of reference with a coverageData >= 11X There is a 1.69% of reference with a coverageData >= 12X There is a 1.62% of reference with a coverageData >= 13X There is a 1.56% of reference with a coverageData >= 14X There is a 1.5% of reference with a coverageData >= 15X There is a 1.45% of reference with a coverageData >= 16X There is a 1.4% of reference with a coverageData >= 17X There is a 1.36% of reference with a coverageData >= 18X There is a 1.32% of reference with a coverageData >= 19X There is a 1.28% of reference with a coverageData >= 20X There is a 1.24% of reference with a coverageData >= 21X There is a 1.21% of reference with a coverageData >= 22X There is a 1.18% of reference with a coverageData >= 23X There is a 1.15% of reference with a coverageData >= 24X There is a 1.12% of reference with a coverageData >= 25X There is a 1.09% of reference with a coverageData >= 26X There is a 1.07% of reference with a coverageData >= 27X There is a 1.04% of reference with a coverageData >= 28X There is a 1.02% of reference with a coverageData >= 29X There is a 1% of reference with a coverageData >= 30X There is a 0.98% of reference with a coverageData >= 31X There is a 0.96% of reference with a coverageData >= 32X There is a 0.94% of reference with a coverageData >= 33X There is a 0.92% of reference with a coverageData >= 34X There is a 0.9% of reference with a coverageData >= 35X There is a 0.88% of reference with a coverageData >= 36X There is a 0.87% of reference with a coverageData >= 37X There is a 0.85% of reference with a coverageData >= 38X There is a 0.84% of reference with a coverageData >= 39X There is a 0.82% of reference with a coverageData >= 40X There is a 0.81% of reference with a coverageData >= 41X There is a 0.79% of reference with a coverageData >= 42X There is a 0.78% of reference with a coverageData >= 43X There is a 0.77% of reference with a coverageData >= 44X There is a 0.75% of reference with a coverageData >= 45X There is a 0.74% of reference with a coverageData >= 46X There is a 0.73% of reference with a coverageData >= 47X There is a 0.72% of reference with a coverageData >= 48X There is a 0.71% of reference with a coverageData >= 49X There is a 0.7% of reference with a coverageData >= 50X There is a 0.69% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 408589049 1.6392699338550494 36.46645365883478 chr2 243199373 564988597 2.323149891508972 88.08992871244683 chr3 198022430 589501336 2.9769422383110844 41.250798380262914 chr4 191154276 290041388 1.5173157204184122 27.924384267532037 chr5 180915260 246754725 1.3639243312034595 26.443378179678366 chr6 171115067 277763697 1.6232568053168572 25.24097975571896 chr7 159138663 275769939 1.7328908877410891 41.851793697559465 chr8 146364022 442255843 3.021615810748901 40.30146817332446 chr9 141213431 120036137 0.8500334291856417 19.61627391306149 chr10 135534747 402169580 2.967280265037865 139.04477647370734 chr11 135006516 148574085 1.1004956605205634 27.150446687250653 chr12 133851895 395653374 2.955904165570461 55.87921539023365 chr13 115169878 204785698 1.7781185632583547 145.21247234415236 chr14 107349540 89542982 0.8341254373330338 17.914190129463055 chr15 102531392 136828340 1.334501925029946 25.96379275090242 chr16 90354753 150242564 1.6628075337663752 28.160130660429676 chr17 81195210 399489259 4.920108698530369 861.7539011660881 chr18 78077248 136602674 1.7495836174963544 24.66114583563481 chr19 59128983 80362432 1.3591039101754887 47.21393287468521 chr20 63025520 112781402 1.7894561123811434 27.12796455060052 chr21 48129895 130495097 2.711310652142499 65.19125337094763 chr22 51304566 281271386 5.482385057111681 611.6398272071544 chrMT 16571 110458564 6665.775390742864 6738.94427739526 chrX 155270560 195322207 1.2579474628029936 36.12223058435606 chrY 59373566 28070527 0.47277818886606876 15.544572706922326