BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472692.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,588,334 number of mapped reads = 19,452,259 (99.31%) number of supplementary alignments = 121,863 (0.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,751,651 number of mapped paired reads (second in pair) = 9,700,608 number of mapped paired reads (both in pair) = 19,360,686 number of mapped paired reads (singletons) = 91,573 number of mapped bases = 1,916,708,648 bp number of sequenced bases = 1,916,476,620 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,471,921 duplication rate = 50.38% >>>>>>> Insert size mean insert size = 19,659.7044 std insert size = 1,341,009.5837 median insert size = 216 >>>>>>> Mapping quality mean mapping quality = 54.964 >>>>>>> ACTG content number of A's = 509,486,435 bp (26.58%) number of C's = 452,056,537 bp (23.59%) number of T's = 509,381,406 bp (26.58%) number of G's = 445,179,120 bp (23.23%) number of N's = 373,122 bp (0.02%) GC percentage = 46.82% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,194,101 number of insertions = 133,182 mapped reads with insertion percentage = 0.68% number of deletions = 97,397 mapped reads with deletion percentage = 0.49% homopolymer indels = 44.16% >>>>>>> Coverage mean coverageData = 0.6192X std coverageData = 32.124X There is a 3.37% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.83% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.24% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.22% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.21% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.2% of reference with a coverageData >= 23X There is a 0.19% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.18% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.17% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.15% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 240839329 0.966253676856436 45.40411309549532 chr2 243199373 125835858 0.5174185132459203 27.362255876639672 chr3 198022430 176662527 0.8921339213946622 37.12673524698477 chr4 191154276 65549497 0.3429141025335996 25.688883846134306 chr5 180915260 82366885 0.45527881395964054 20.39424674435843 chr6 171115067 187207916 1.0940469432770639 54.50156036625548 chr7 159138663 81030759 0.5091833591689783 23.898259751776774 chr8 146364022 77477655 0.5293490431685459 28.170874029196007 chr9 141213431 91389798 0.6471749702052066 26.828545579419323 chr10 135534747 41273661 0.30452457331845684 21.349709089939935 chr11 135006516 103670428 0.7678920327075176 35.34112868588807 chr12 133851895 107399736 0.8023774037715342 35.587159833176244 chr13 115169878 38169058 0.33141528551415156 15.56365059220381 chr14 107349540 38387362 0.3575922356071577 17.383542857404564 chr15 102531392 47356555 0.4618737157104041 23.296754531080516 chr16 90354753 121506517 1.344771724405024 57.723840369803405 chr17 81195210 79403023 0.9779274294628957 34.30581537999925 chr18 78077248 25247054 0.32335993707155253 17.45301050210494 chr19 59128983 60910348 1.030126765413841 36.94047563780697 chr20 63025520 39300839 0.6235702458305779 23.861375260036425 chr21 48129895 8196784 0.17030546191717227 11.602436382151307 chr22 51304566 37572809 0.7323482475224525 49.598103570486344 chrMT 16571 5490 0.33130167159495505 0.7177223121094232 chrX 155270560 37294872 0.24019280924857875 11.548086735965848 chrY 59373566 2653888 0.044698140583302674 3.7244329914356666