BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163084.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 = 90,557,844 number of mapped reads = 89,178,100 (98.48%) number of supplementary alignments = 581,589 (0.64%) number of secondary alignments = 0 number of mapped bases = 8,464,585,779 bp number of sequenced bases = 8,463,525,523 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,211,795 duplication rate = 47.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1367 >>>>>>> ACTG content number of A's = 2,110,250,305 bp (24.93%) number of C's = 2,122,543,450 bp (25.08%) number of T's = 2,080,877,457 bp (24.59%) number of G's = 2,149,522,484 bp (25.4%) number of N's = 331,827 bp (0%) GC percentage = 50.48% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 31,376,894 number of insertions = 556,249 mapped reads with insertion percentage = 0.62% number of deletions = 496,952 mapped reads with deletion percentage = 0.55% homopolymer indels = 45.89% >>>>>>> Coverage mean coverageData = 2.7343X std coverageData = 34.6478X There is a 10.53% of reference with a coverageData >= 1X There is a 6.55% of reference with a coverageData >= 2X There is a 4.61% of reference with a coverageData >= 3X There is a 4.04% of reference with a coverageData >= 4X There is a 3.61% of reference with a coverageData >= 5X There is a 3.36% of reference with a coverageData >= 6X There is a 3.16% of reference with a coverageData >= 7X There is a 3% of reference with a coverageData >= 8X There is a 2.87% of reference with a coverageData >= 9X There is a 2.75% of reference with a coverageData >= 10X There is a 2.65% of reference with a coverageData >= 11X There is a 2.56% of reference with a coverageData >= 12X There is a 2.47% of reference with a coverageData >= 13X There is a 2.4% of reference with a coverageData >= 14X There is a 2.33% of reference with a coverageData >= 15X There is a 2.26% 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 2.09% of reference with a coverageData >= 19X There is a 2.04% of reference with a coverageData >= 20X There is a 1.99% of reference with a coverageData >= 21X There is a 1.94% of reference with a coverageData >= 22X There is a 1.9% of reference with a coverageData >= 23X There is a 1.86% of reference with a coverageData >= 24X There is a 1.82% of reference with a coverageData >= 25X There is a 1.78% of reference with a coverageData >= 26X There is a 1.74% of reference with a coverageData >= 27X There is a 1.71% of reference with a coverageData >= 28X There is a 1.68% of reference with a coverageData >= 29X There is a 1.64% of reference with a coverageData >= 30X There is a 1.61% of reference with a coverageData >= 31X There is a 1.58% of reference with a coverageData >= 32X There is a 1.55% of reference with a coverageData >= 33X There is a 1.53% of reference with a coverageData >= 34X There is a 1.5% of reference with a coverageData >= 35X There is a 1.47% of reference with a coverageData >= 36X There is a 1.45% of reference with a coverageData >= 37X There is a 1.42% of reference with a coverageData >= 38X There is a 1.4% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.36% of reference with a coverageData >= 41X There is a 1.33% of reference with a coverageData >= 42X There is a 1.31% of reference with a coverageData >= 43X There is a 1.29% of reference with a coverageData >= 44X There is a 1.27% of reference with a coverageData >= 45X There is a 1.25% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.22% of reference with a coverageData >= 48X There is a 1.2% of reference with a coverageData >= 49X There is a 1.18% of reference with a coverageData >= 50X There is a 1.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1257663875 5.0457803072033265 50.93033060113616 chr2 243199373 379032665 1.5585264892932105 19.778464855254523 chr3 198022430 380903435 1.9235368185311128 23.883260579629134 chr4 191154276 182392883 0.9541658539723171 15.058307044706346 chr5 180915260 446558537 2.4683298523297594 36.8100865682683 chr6 171115067 488447294 2.8544961151784487 31.40610951056325 chr7 159138663 541936734 3.405437269508793 42.539858450823125 chr8 146364022 426059093 2.910955077471156 49.10998934239501 chr9 141213431 382596937 2.709352320743485 30.03232700626804 chr10 135534747 194462053 1.4347763750944251 16.82890742837855 chr11 135006516 473924950 3.510385750566291 34.65815969416454 chr12 133851895 243258812 1.8173729404428678 23.697285073780897 chr13 115169878 116081001 1.007911122385664 14.522812664055968 chr14 107349540 252874120 2.3556143789717217 26.36804198814991 chr15 102531392 398567408 3.887271987880551 37.75094892972252 chr16 90354753 324672351 3.5933068291382524 33.10379442984032 chr17 81195210 230941513 2.844275087163393 29.136292600629158 chr18 78077248 137978065 1.7671993895071711 21.22631565529058 chr19 59128983 635563958 10.748772019298894 85.66736641243156 chr20 63025520 213934099 3.394404346049029 35.133459111830014 chr21 48129895 115579136 2.4014001277168795 46.64522716382157 chr22 51304566 101303618 1.9745536488896525 21.148433572550843 chrMT 16571 3020 0.1822460925713596 0.5060503404824837 chrX 155270560 530609580 3.4173225111057755 41.04761797491319 chrY 59373566 9240642 0.1556356241092206 7.407941141341028