BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063586.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,751,239 number of mapped reads = 2,386,412 (86.74%) number of supplementary alignments = 26,072 (0.95%) number of secondary alignments = 0 number of mapped bases = 158,652,871 bp number of sequenced bases = 158,587,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 298,893 duplication rate = 9.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.5631 >>>>>>> ACTG content number of A's = 44,472,231 bp (28.04%) number of C's = 28,868,884 bp (18.2%) number of T's = 50,779,150 bp (32.02%) number of G's = 34,462,737 bp (21.73%) number of N's = 4,156 bp (0%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,236,505 number of insertions = 11,891 mapped reads with insertion percentage = 0.49% number of deletions = 41,500 mapped reads with deletion percentage = 1.72% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.5595X There is a 2.74% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.57% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 7319048 0.029364211694381297 0.582134293933553 chr2 243199373 40392211 0.16608682210706194 0.9062171796374316 chr3 198022430 2321341 0.011722616473295474 0.16941493791666987 chr4 191154276 11396309 0.05961838384405275 0.4008863183287608 chr5 180915260 3315322 0.018325275601405875 0.2170578589803998 chr6 171115067 6322158 0.03694682245602604 0.3274273291762958 chr7 159138663 13803366 0.08673797894104464 0.7987206714537367 chr8 146364022 3226279 0.022042841921903457 0.5903410631948863 chr9 141213431 6353545 0.044992497916150766 0.38288953124862296 chr10 135534747 9918221 0.07317843740837912 0.4791122461216749 chr11 135006516 22713041 0.16823662792690688 1.3777157702399416 chr12 133851895 6074601 0.04538300335606007 0.34866303752164923 chr13 115169878 1306260 0.01134202816469077 0.173530285252095 chr14 107349540 3103094 0.028906448970344913 0.2956544058277877 chr15 102531392 2179328 0.021255226887000617 0.2370238012074304 chr16 90354753 1812583 0.020060737701313842 0.25218299310280184 chr17 81195210 2780379 0.03424314069758549 0.5198931890789107 chr18 78077248 2799236 0.03585213454244699 0.7351360986899387 chr19 59128983 1450963 0.02453894733822836 0.364801079769747 chr20 63025520 1182697 0.018765366791103032 0.2833887245094711 chr21 48129895 3337248 0.06933836028522397 0.44841058358840064 chr22 51304566 538234 0.010490957081675733 0.15347011206713204 chrMT 16571 103839 6.266308611429606 5.110888056644355 chrX 155270560 4488374 0.028906793406296726 0.387840980277336 chrY 59373566 415194 0.006992909942448126 0.11908792330506489