BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068127.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 = 4,369,502 number of mapped reads = 4,119,217 (94.27%) number of supplementary alignments = 32,274 (0.74%) number of secondary alignments = 0 number of mapped bases = 266,369,657 bp number of sequenced bases = 266,257,175 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 371,448 duplication rate = 7.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1807 >>>>>>> ACTG content number of A's = 71,403,089 bp (26.82%) number of C's = 48,036,033 bp (18.04%) number of T's = 85,322,812 bp (32.05%) number of G's = 61,465,318 bp (23.08%) number of N's = 29,923 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,575,385 number of insertions = 17,805 mapped reads with insertion percentage = 0.43% number of deletions = 64,579 mapped reads with deletion percentage = 1.55% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.086X std coverageData = 1.0676X There is a 6.73% of reference with a coverageData >= 1X There is a 1.26% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 26153673 0.10492921901285855 2.4618380315808417 chr2 243199373 26729897 0.10990939931411747 1.1271270247089824 chr3 198022430 10457641 0.05281038617695985 0.284751771464836 chr4 191154276 15532193 0.08125475048227537 0.3765302055486763 chr5 180915260 13869585 0.07666343347708757 0.35131413879271295 chr6 171115067 17628222 0.10301969492844251 0.5938138811043241 chr7 159138663 23408603 0.14709563696661193 2.2290924120526556 chr8 146364022 14286970 0.09761258132138512 1.2727694577121067 chr9 141213431 8184854 0.05796087484058085 0.6788045636303502 chr10 135534747 14685663 0.10835349107930234 0.6160127327528188 chr11 135006516 11528664 0.08539338945684666 0.46119972297457273 chr12 133851895 15227796 0.11376600981256187 0.458241640973414 chr13 115169878 6827021 0.05927783478245935 0.3276835874677947 chr14 107349540 5858954 0.05457828696797397 0.36125842436592837 chr15 102531392 8137543 0.07936635640331499 0.390017968076429 chr16 90354753 4515055 0.04997030980760912 0.3403227150593749 chr17 81195210 6505080 0.080116548747149 0.36778618147032316 chr18 78077248 6356563 0.0814137685795483 1.2516339842007502 chr19 59128983 6143343 0.10389732223197548 1.4544008289866357 chr20 63025520 4096728 0.06500109796793425 0.3680265780579968 chr21 48129895 6753098 0.14030984277027822 0.4825220448228941 chr22 51304566 2097414 0.04088162445424448 0.23927327309805957 chrMT 16571 211586 12.768450908213143 7.488844267324733 chrX 155270560 10562199 0.06802447933465301 0.44062333447743185 chrY 59373566 611312 0.010296029718006158 0.45303733527731627