BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163074.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 = 93,070,840 number of mapped reads = 91,956,368 (98.8%) number of supplementary alignments = 546,441 (0.59%) number of secondary alignments = 0 number of mapped bases = 9,036,543,449 bp number of sequenced bases = 9,035,317,056 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,224,073 duplication rate = 45.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.9222 >>>>>>> ACTG content number of A's = 2,221,944,697 bp (24.59%) number of C's = 2,295,380,066 bp (25.4%) number of T's = 2,214,225,077 bp (24.51%) number of G's = 2,303,109,187 bp (25.49%) number of N's = 658,029 bp (0.01%) GC percentage = 50.89% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 32,381,724 number of insertions = 614,094 mapped reads with insertion percentage = 0.66% number of deletions = 551,795 mapped reads with deletion percentage = 0.59% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 2.9191X std coverageData = 35.6636X There is a 10.9% of reference with a coverageData >= 1X There is a 6.73% of reference with a coverageData >= 2X There is a 5.05% of reference with a coverageData >= 3X There is a 4.46% of reference with a coverageData >= 4X There is a 4.04% of reference with a coverageData >= 5X There is a 3.77% of reference with a coverageData >= 6X There is a 3.56% of reference with a coverageData >= 7X There is a 3.38% of reference with a coverageData >= 8X There is a 3.23% of reference with a coverageData >= 9X There is a 3.1% of reference with a coverageData >= 10X There is a 2.98% of reference with a coverageData >= 11X There is a 2.87% of reference with a coverageData >= 12X There is a 2.78% of reference with a coverageData >= 13X There is a 2.69% of reference with a coverageData >= 14X There is a 2.61% of reference with a coverageData >= 15X There is a 2.53% of reference with a coverageData >= 16X There is a 2.46% of reference with a coverageData >= 17X There is a 2.39% of reference with a coverageData >= 18X There is a 2.33% of reference with a coverageData >= 19X There is a 2.27% of reference with a coverageData >= 20X There is a 2.22% of reference with a coverageData >= 21X There is a 2.17% of reference with a coverageData >= 22X There is a 2.11% of reference with a coverageData >= 23X There is a 2.07% of reference with a coverageData >= 24X There is a 2.02% of reference with a coverageData >= 25X There is a 1.98% of reference with a coverageData >= 26X There is a 1.94% of reference with a coverageData >= 27X There is a 1.9% of reference with a coverageData >= 28X There is a 1.86% of reference with a coverageData >= 29X There is a 1.82% of reference with a coverageData >= 30X There is a 1.79% of reference with a coverageData >= 31X There is a 1.75% of reference with a coverageData >= 32X There is a 1.72% of reference with a coverageData >= 33X There is a 1.69% of reference with a coverageData >= 34X There is a 1.66% of reference with a coverageData >= 35X There is a 1.63% of reference with a coverageData >= 36X There is a 1.6% of reference with a coverageData >= 37X There is a 1.57% of reference with a coverageData >= 38X There is a 1.54% of reference with a coverageData >= 39X There is a 1.52% of reference with a coverageData >= 40X There is a 1.49% of reference with a coverageData >= 41X There is a 1.47% of reference with a coverageData >= 42X There is a 1.44% of reference with a coverageData >= 43X There is a 1.42% of reference with a coverageData >= 44X There is a 1.4% of reference with a coverageData >= 45X There is a 1.38% of reference with a coverageData >= 46X There is a 1.35% of reference with a coverageData >= 47X There is a 1.33% of reference with a coverageData >= 48X There is a 1.31% of reference with a coverageData >= 49X There is a 1.29% of reference with a coverageData >= 50X There is a 1.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1333157168 5.348661370035263 52.173041570534025 chr2 243199373 402603644 1.6554468830805744 18.753443874453527 chr3 198022430 393450410 1.9868982013805203 23.417388754592928 chr4 191154276 191705177 1.0028819705817096 21.266965072193116 chr5 180915260 496834662 2.746228604485879 39.1251712950615 chr6 171115067 535909242 3.1318647235196417 35.30802077845348 chr7 159138663 615930261 3.870399872594129 53.88090195212614 chr8 146364022 442293497 3.021873073425107 49.07076007290159 chr9 141213431 431375197 3.05477456319293 32.15839357759746 chr10 135534747 204100744 1.5058923893516398 17.782109774677096 chr11 135006516 486653212 3.6046646222616396 32.18137470703447 chr12 133851895 230553039 1.722448823006951 19.333905869125584 chr13 115169878 123635275 1.073503568354913 14.534242230946285 chr14 107349540 256897999 2.393098275036856 24.690533296707425 chr15 102531392 393506934 3.837916625573561 35.05186698194083 chr16 90354753 361637340 4.002416342170732 32.87248598732509 chr17 81195210 254024140 3.1285606626302216 27.71793890935882 chr18 78077248 156022115 1.998304486858963 22.776613311519817 chr19 59128983 727179822 12.298195996369497 86.23515152677739 chr20 63025520 230165171 3.651936088746273 35.24683930129408 chr21 48129895 121531891 2.5250811579788404 44.37006086417804 chr22 51304566 98434867 1.9186375536243694 17.389437791233913 chrMT 16571 749 0.04519944481322793 0.23957921995283346 chrX 155270560 539816400 3.4766178469376294 39.10357115079428 chrY 59373566 9124493 0.1536793831787028 7.147134726037231