BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089529.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 8,771,376 number of mapped reads = 6,612,834 (75.39%) number of supplementary alignments = 266 (0%) number of secondary alignments = 0 number of mapped bases = 308,378,703 bp number of sequenced bases = 308,317,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,913,788 duplication rate = 21.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.075 >>>>>>> ACTG content number of A's = 99,955,958 bp (32.42%) number of C's = 59,856,618 bp (19.41%) number of T's = 77,585,768 bp (25.16%) number of G's = 70,881,740 bp (22.99%) number of N's = 37,770 bp (0.01%) GC percentage = 42.4% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 2,576,858 number of insertions = 16,998 mapped reads with insertion percentage = 0.26% number of deletions = 41,008 mapped reads with deletion percentage = 0.62% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0996X std coverageData = 0.9093X There is a 3.84% of reference with a coverageData >= 1X There is a 1.7% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 19336101 0.07757694212525151 0.8659401757163574 chr2 243199373 27294790 0.1122321561248433 1.036477613163262 chr3 198022430 21556389 0.10885831973680961 0.8979321929329531 chr4 191154276 21200722 0.11090896025783907 0.9405637222525887 chr5 180915260 19726888 0.10903938119979487 0.8926836519167983 chr6 171115067 13951232 0.08153128911786593 0.8086575895320643 chr7 159138663 18121344 0.11387141036870468 1.0229506453686317 chr8 146364022 16650169 0.11375861890430969 1.0794781714978763 chr9 141213431 13345817 0.0945081279131303 0.84879962533581 chr10 135534747 14824632 0.10937882962219275 0.9407752657437715 chr11 135006516 14845118 0.1099585297053366 1.0319101888314397 chr12 133851895 14924473 0.11149990069247806 0.8976099341800843 chr13 115169878 10176529 0.088361029608801 0.8151452038055663 chr14 107349540 6785495 0.06320935329578496 0.7491804433468526 chr15 102531392 9101166 0.08876467804123833 0.7805829700869292 chr16 90354753 8213105 0.0908984278890121 0.8170249627083794 chr17 81195210 8954069 0.11027829104697186 0.9035286722346738 chr18 78077248 8177515 0.10473620945246431 0.9211312202504799 chr19 59128983 6572293 0.11115180181604004 0.9255383337160298 chr20 63025520 7019823 0.11138064390424704 0.8979731671689234 chr21 48129895 4127601 0.08575960949011005 0.9218083607575925 chr22 51304566 3563711 0.06946186816978435 0.6867529644199175 chrMT 16571 9763 0.5891617886669482 1.6650085713803926 chrX 155270560 18934307 0.1219439602716703 0.98146775612212 chrY 59373566 965651 0.016263988590478125 0.34530009993098226