BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038440.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 18,060,414 number of mapped reads = 17,227,941 (95.39%) number of supplementary alignments = 283,315 (1.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,741,664 number of mapped paired reads (second in pair) = 8,486,277 number of mapped paired reads (both in pair) = 16,925,480 number of mapped paired reads (singletons) = 302,461 number of mapped bases = 2,333,238,996 bp number of sequenced bases = 2,331,583,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,508,868 duplication rate = 14.44% >>>>>>> Insert size mean insert size = 89,228.7344 std insert size = 2,893,393.3291 median insert size = 273 >>>>>>> Mapping quality mean mapping quality = 53.4148 >>>>>>> ACTG content number of A's = 673,831,349 bp (28.9%) number of C's = 455,254,934 bp (19.53%) number of T's = 690,031,886 bp (29.59%) number of G's = 512,277,921 bp (21.97%) number of N's = 187,100 bp (0.01%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 30,078,894 number of insertions = 422,641 mapped reads with insertion percentage = 2.32% number of deletions = 836,864 mapped reads with deletion percentage = 4.68% homopolymer indels = 47.62% >>>>>>> Coverage mean coverageData = 0.7537X std coverageData = 9.8785X There is a 28.49% of reference with a coverageData >= 1X There is a 16.42% of reference with a coverageData >= 2X There is a 9.53% of reference with a coverageData >= 3X There is a 5.88% of reference with a coverageData >= 4X There is a 3.65% of reference with a coverageData >= 5X There is a 2.33% of reference with a coverageData >= 6X There is a 1.51% of reference with a coverageData >= 7X There is a 1% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.46% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 199832194 0.8017319804390778 14.25218927029338 chr2 243199373 211479398 0.8695721349577658 10.84867797006024 chr3 198022430 163013788 0.8232087041856824 1.8069849092702055 chr4 191154276 103212979 0.5399459596708158 10.059399140641288 chr5 180915260 163739860 0.9050638403858249 1.8260294241467057 chr6 171115067 139997803 0.8181500638982305 7.948425270982469 chr7 159138663 114044969 0.716638979177549 10.81411897356253 chr8 146364022 151304956 1.0337578452169072 3.9217346007721905 chr9 141213431 100194475 0.7095251088403907 17.345581437814943 chr10 135534747 123832255 0.9136568868203222 23.62014377172087 chr11 135006516 107268153 0.7945405612866864 8.080729574555036 chr12 133851895 97465096 0.7281562655500694 1.7767386697828182 chr13 115169878 80501261 0.6989784342742813 1.5575737890903498 chr14 107349540 76720316 0.7146776409102452 1.6641951592678346 chr15 102531392 63358653 0.6179439463769301 1.4838218916664982 chr16 90354753 71815331 0.7948151991517258 9.199303189215874 chr17 81195210 56141467 0.6914381648868203 11.804998276836658 chr18 78077248 93967711 1.2035223244548783 11.835606567365733 chr19 59128983 30341723 0.5131446789808646 5.976505111786611 chr20 63025520 59691893 0.9471067116939297 3.4352955792466235 chr21 48129895 22756465 0.47281351850030007 4.405232429514392 chr22 51304566 12080549 0.23546732663131775 0.9497880606997251 chrMT 16571 5731358 345.8667551747028 174.58204087904602 chrX 155270560 79646107 0.5129504717442894 2.376002093845466 chrY 59373566 5100236 0.08590078621856737 9.385326449688556