BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163027.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 = 69,337,662 number of mapped reads = 68,113,656 (98.23%) number of supplementary alignments = 369,692 (0.53%) number of secondary alignments = 0 number of mapped bases = 6,629,050,128 bp number of sequenced bases = 6,628,222,858 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,586,342 duplication rate = 43.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.035 >>>>>>> ACTG content number of A's = 1,585,052,096 bp (23.91%) number of C's = 1,729,990,218 bp (26.1%) number of T's = 1,585,530,508 bp (23.92%) number of G's = 1,726,117,585 bp (26.04%) number of N's = 1,532,451 bp (0.02%) GC percentage = 52.14% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 29,052,222 number of insertions = 437,514 mapped reads with insertion percentage = 0.63% number of deletions = 375,102 mapped reads with deletion percentage = 0.54% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 2.1414X std coverageData = 25.4625X There is a 8.68% of reference with a coverageData >= 1X There is a 6% of reference with a coverageData >= 2X There is a 4.54% of reference with a coverageData >= 3X There is a 4.07% of reference with a coverageData >= 4X There is a 3.69% of reference with a coverageData >= 5X There is a 3.45% of reference with a coverageData >= 6X There is a 3.25% of reference with a coverageData >= 7X There is a 3.09% of reference with a coverageData >= 8X There is a 2.95% of reference with a coverageData >= 9X There is a 2.82% of reference with a coverageData >= 10X There is a 2.71% of reference with a coverageData >= 11X There is a 2.61% of reference with a coverageData >= 12X There is a 2.51% of reference with a coverageData >= 13X There is a 2.43% of reference with a coverageData >= 14X There is a 2.35% of reference with a coverageData >= 15X There is a 2.27% of reference with a coverageData >= 16X There is a 2.2% of reference with a coverageData >= 17X There is a 2.14% of reference with a coverageData >= 18X There is a 2.08% of reference with a coverageData >= 19X There is a 2.02% of reference with a coverageData >= 20X There is a 1.96% of reference with a coverageData >= 21X There is a 1.91% of reference with a coverageData >= 22X There is a 1.86% of reference with a coverageData >= 23X There is a 1.81% of reference with a coverageData >= 24X There is a 1.76% of reference with a coverageData >= 25X There is a 1.72% of reference with a coverageData >= 26X There is a 1.68% of reference with a coverageData >= 27X There is a 1.64% of reference with a coverageData >= 28X There is a 1.6% of reference with a coverageData >= 29X There is a 1.56% of reference with a coverageData >= 30X There is a 1.53% of reference with a coverageData >= 31X There is a 1.49% of reference with a coverageData >= 32X There is a 1.46% of reference with a coverageData >= 33X There is a 1.43% of reference with a coverageData >= 34X There is a 1.4% of reference with a coverageData >= 35X There is a 1.37% of reference with a coverageData >= 36X There is a 1.34% of reference with a coverageData >= 37X There is a 1.31% of reference with a coverageData >= 38X There is a 1.28% of reference with a coverageData >= 39X There is a 1.26% of reference with a coverageData >= 40X There is a 1.23% of reference with a coverageData >= 41X There is a 1.21% of reference with a coverageData >= 42X There is a 1.19% of reference with a coverageData >= 43X There is a 1.16% of reference with a coverageData >= 44X There is a 1.14% of reference with a coverageData >= 45X There is a 1.12% of reference with a coverageData >= 46X There is a 1.1% of reference with a coverageData >= 47X There is a 1.08% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 1.04% of reference with a coverageData >= 50X There is a 1.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 994636870 3.990509094859988 37.18268018957984 chr2 243199373 286428575 1.177752111227688 13.72058930206025 chr3 198022430 281852392 1.4233356898003928 14.893719977548612 chr4 191154276 138836863 0.7263079116263138 10.982034145584093 chr5 180915260 354833089 1.9613220521032886 25.59633676038363 chr6 171115067 365766532 2.13754719799163 23.497461808672348 chr7 159138663 419946558 2.6388719754419454 26.737111933692137 chr8 146364022 329565321 2.2516825958772846 44.17040563949671 chr9 141213431 166696627 1.1804587270455882 13.621215981890117 chr10 135534747 143962716 1.062183087263962 10.440557310393523 chr11 135006516 385040699 2.85201566863632 24.173391555064388 chr12 133851895 185519813 1.3860081174046883 14.602098869398402 chr13 115169878 95019377 0.8250367079489309 10.991382909242322 chr14 107349540 197882102 1.8433437348683561 17.652664522633014 chr15 102531392 323438699 3.1545333842731793 27.5460293413154 chr16 90354753 301182529 3.333333543615575 26.626294931438395 chr17 81195210 206024878 2.5374018738297495 20.049207228597506 chr18 78077248 106783051 1.3676590009934777 15.35510761295952 chr19 59128983 626273248 10.591645860034495 71.11458052278009 chr20 63025520 169810721 2.6943168576792385 23.58203692958072 chr21 48129895 99806860 2.073697854524719 45.76362737383912 chr22 51304566 77924431 1.5188595689514264 14.383361902685003 chrMT 16571 9620 0.5805322551445296 1.067156638875794 chrX 155270560 364393054 2.3468264299426758 24.476249764991735 chrY 59373566 7415503 0.12489569853358648 7.249578277644797