BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153395.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 = 48,389,698 number of mapped reads = 47,981,297 (99.16%) number of supplementary alignments = 311,901 (0.64%) number of secondary alignments = 0 number of mapped bases = 4,115,826,753 bp number of sequenced bases = 4,115,076,907 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,898,212 duplication rate = 44.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.843 >>>>>>> ACTG content number of A's = 1,076,555,068 bp (26.16%) number of C's = 989,479,843 bp (24.05%) number of T's = 1,112,570,258 bp (27.04%) number of G's = 934,617,633 bp (22.71%) number of N's = 1,854,105 bp (0.05%) GC percentage = 46.76% >>>>>>> Mismatches and indels general error rate = 0.0026 number of mismatches = 9,999,985 number of insertions = 448,910 mapped reads with insertion percentage = 0.93% number of deletions = 365,078 mapped reads with deletion percentage = 0.75% homopolymer indels = 49.3% >>>>>>> Coverage mean coverageData = 1.3295X std coverageData = 14.1709X There is a 17.63% of reference with a coverageData >= 1X There is a 12.54% of reference with a coverageData >= 2X There is a 5.34% of reference with a coverageData >= 3X There is a 4.15% of reference with a coverageData >= 4X There is a 2.72% of reference with a coverageData >= 5X There is a 2.32% of reference with a coverageData >= 6X There is a 1.95% of reference with a coverageData >= 7X There is a 1.78% of reference with a coverageData >= 8X There is a 1.63% of reference with a coverageData >= 9X There is a 1.53% of reference with a coverageData >= 10X There is a 1.44% of reference with a coverageData >= 11X There is a 1.38% of reference with a coverageData >= 12X There is a 1.32% of reference with a coverageData >= 13X There is a 1.26% of reference with a coverageData >= 14X There is a 1.22% of reference with a coverageData >= 15X There is a 1.18% of reference with a coverageData >= 16X There is a 1.14% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 1.07% of reference with a coverageData >= 19X There is a 1.04% of reference with a coverageData >= 20X There is a 1.01% of reference with a coverageData >= 21X There is a 0.98% of reference with a coverageData >= 22X There is a 0.95% of reference with a coverageData >= 23X There is a 0.93% of reference with a coverageData >= 24X There is a 0.91% of reference with a coverageData >= 25X There is a 0.88% of reference with a coverageData >= 26X There is a 0.86% of reference with a coverageData >= 27X There is a 0.84% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.8% of reference with a coverageData >= 30X There is a 0.79% of reference with a coverageData >= 31X There is a 0.77% of reference with a coverageData >= 32X There is a 0.75% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.7% of reference with a coverageData >= 36X There is a 0.69% of reference with a coverageData >= 37X There is a 0.68% of reference with a coverageData >= 38X There is a 0.66% of reference with a coverageData >= 39X There is a 0.65% of reference with a coverageData >= 40X There is a 0.64% of reference with a coverageData >= 41X There is a 0.62% of reference with a coverageData >= 42X There is a 0.61% of reference with a coverageData >= 43X There is a 0.6% of reference with a coverageData >= 44X There is a 0.59% of reference with a coverageData >= 45X There is a 0.58% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 456233636 1.8304212610166375 19.80771901801284 chr2 243199373 311069759 1.2790730303404194 13.335398450965467 chr3 198022430 223328014 1.1277915032150652 11.491970484470857 chr4 191154276 169103239 0.8846427217772518 9.474054884046511 chr5 180915260 203550063 1.1251127351004 12.56479395296368 chr6 171115067 212085307 1.23943093216917 14.079495969169091 chr7 159138663 201480503 1.2660688433708909 12.861695435893491 chr8 146364022 158024318 1.0796664087298722 13.004493432156622 chr9 141213431 164378608 1.164043723291448 12.901444204821713 chr10 135534747 163279031 1.2047023705293816 11.192399577226821 chr11 135006516 195701414 1.4495701377850532 14.123778528044342 chr12 133851895 220229142 1.645319567571307 15.951077520235366 chr13 115169878 81165302 0.7047441866700597 8.45562219810369 chr14 107349540 127042964 1.1834514055672711 12.678149601507787 chr15 102531392 150386835 1.4667394255215027 14.023280891328076 chr16 90354753 148424304 1.6426839659447687 14.619262778463689 chr17 81195210 192662071 2.372825576779714 20.375075555935048 chr18 78077248 72432364 0.9277012939800338 10.198287841704788 chr19 59128983 167030966 2.8248577520773526 21.218000076492658 chr20 63025520 93427798 1.4823804389079218 15.595773310049214 chr21 48129895 32232798 0.669704307478751 7.474740978906732 chr22 51304566 66154679 1.2894501241858278 13.368862382426066 chrMT 16571 4929 0.2974473477762356 1.1285403869214676 chrX 155270560 302914067 1.950878949621873 19.75362195463573 chrY 59373566 3484642 0.05869012482760426 2.8212115967411675