BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013351.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 = 2,076,448 number of mapped reads = 1,859,559 (89.55%) number of supplementary alignments = 22,593 (1.09%) number of secondary alignments = 0 number of mapped bases = 120,503,408 bp number of sequenced bases = 120,426,215 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,921 duplication rate = 6.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2143 >>>>>>> ACTG content number of A's = 33,136,653 bp (27.52%) number of C's = 21,870,024 bp (18.16%) number of T's = 38,675,933 bp (32.12%) number of G's = 26,730,229 bp (22.2%) number of N's = 13,376 bp (0.01%) GC percentage = 40.36% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,005,197 number of insertions = 9,047 mapped reads with insertion percentage = 0.48% number of deletions = 44,892 mapped reads with deletion percentage = 2.38% homopolymer indels = 44.3% >>>>>>> Coverage mean coverageData = 0.0389X std coverageData = 0.3778X There is a 2.76% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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% 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 9045734 0.036291721014408224 0.6520468915400536 chr2 243199373 15609963 0.0641858686041925 0.5462033057038036 chr3 198022430 7106807 0.03588889905047625 0.2529983287406284 chr4 191154276 5221420 0.027315214230415646 0.24301912711129472 chr5 180915260 8248636 0.045593920601280404 0.28581861728932684 chr6 171115067 3690131 0.021565202087084477 0.2308476485379144 chr7 159138663 4207825 0.026441248912591406 0.26070963170196026 chr8 146364022 7739226 0.052876560060641134 0.45236038124043254 chr9 141213431 4929903 0.034911006446688486 0.33690369488447186 chr10 135534747 3854116 0.02843636842440116 0.4140899341063167 chr11 135006516 5459634 0.0404397814398825 0.2951519791074733 chr12 133851895 7851961 0.05866156022669683 0.33117359385269113 chr13 115169878 1896148 0.01646392297124774 0.1699720016489266 chr14 107349540 5811598 0.05413714860818221 0.32673083693593735 chr15 102531392 3631794 0.03542128834064791 0.250955925175558 chr16 90354753 2704042 0.029926948059943233 0.2580298684665982 chr17 81195210 3500580 0.04311313438317359 0.2961600814021857 chr18 78077248 4564927 0.058466802006136284 0.645381553497097 chr19 59128983 2641081 0.0446664371007362 0.5047571657299191 chr20 63025520 3984566 0.06322146965229324 0.3534862575467801 chr21 48129895 2560090 0.053191265013148276 0.32821775757684124 chr22 51304566 610763 0.01190465191733617 0.13824960641918083 chrMT 16571 5687 0.3431899100838815 0.6050936895580873 chrX 155270560 5322722 0.034280304006116806 0.2638650484181593 chrY 59373566 304054 0.0051210331547207385 0.15817201257804256