BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124784.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 773,471 number of mapped reads = 772,461 (99.87%) number of supplementary alignments = 360,445 (46.6%) number of secondary alignments = 0 number of mapped bases = 116,367,585 bp number of sequenced bases = 116,313,848 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,130,827 duplication rate = 28.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1094 >>>>>>> ACTG content number of A's = 32,426,830 bp (27.88%) number of C's = 21,403,097 bp (18.4%) number of T's = 37,656,116 bp (32.37%) number of G's = 24,827,805 bp (21.35%) number of N's = 0 bp (0%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 890,194 number of insertions = 16,518 mapped reads with insertion percentage = 2.12% number of deletions = 51,793 mapped reads with deletion percentage = 6.46% homopolymer indels = 80.17% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 70.562X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% 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 110513 4.433810417667926E-4 0.3637090766165658 chr2 243199373 13502 5.551823523821338E-5 0.018150555682667976 chr3 198022430 22450 1.1337099539683459E-4 0.1109850106289385 chr4 191154276 9737 5.093791362532743E-5 0.007225771795050449 chr5 180915260 8552 4.72707498527211E-5 0.006882843699797603 chr6 171115067 8529 4.9843652867809704E-5 0.009953158312360669 chr7 159138663 12540 7.879920418836244E-5 0.01916169187050705 chr8 146364022 86174680 0.5887695543102799 305.76111733811405 chr9 141213431 5526 3.913225506148916E-5 0.006252624976946774 chr10 135534747 29935228 0.22086755361708094 112.9726574279757 chr11 135006516 9103 6.742637518325412E-5 0.011912166744475825 chr12 133851895 7885 5.8908392742590605E-5 0.00767252059139044 chr13 115169878 4032 3.500915404286527E-5 0.005916749817424975 chr14 107349540 6295 5.864021401489005E-5 0.03125180277951756 chr15 102531392 3919 3.822244020641015E-5 0.009206143078595562 chr16 90354753 3648 4.037419038708456E-5 0.006346969951881626 chr17 81195210 5158 6.352591489079221E-5 0.00818429486630399 chr18 78077248 4555 5.833965869288836E-5 0.007636979039060405 chr19 59128983 4286 7.24856032108653E-5 0.012356290151595816 chr20 63025520 4643 7.366857108041314E-5 0.013876864174963546 chr21 48129895 1349 2.802831795082869E-5 0.0052685334874512995 chr22 51304566 1892 3.687780927724834E-5 0.006070993271244757 chrMT 16571 0 0.0 0.0 chrX 155270560 6540 4.2120025843920445E-5 0.008672676545857757 chrY 59373566 3023 5.091491388608863E-5 0.0072372413930691425