BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514764.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 14,268,265 number of mapped reads = 10,952,130 (76.76%) number of supplementary alignments = 1,944,273 (13.63%) number of secondary alignments = 0 number of mapped bases = 1,004,952,984 bp number of sequenced bases = 1,003,836,663 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,313,300 duplication rate = 31.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8844 >>>>>>> ACTG content number of A's = 308,171,484 bp (30.7%) number of C's = 187,816,632 bp (18.71%) number of T's = 308,608,610 bp (30.74%) number of G's = 199,173,451 bp (19.84%) number of N's = 66,486 bp (0.01%) GC percentage = 38.55% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 6,252,594 number of insertions = 665,822 mapped reads with insertion percentage = 5.79% number of deletions = 358,181 mapped reads with deletion percentage = 3.02% homopolymer indels = 39.73% >>>>>>> Coverage mean coverageData = 0.3246X std coverageData = 38.1619X There is a 2.3% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.93% of reference with a coverageData >= 4X There is a 0.81% of reference with a coverageData >= 5X There is a 0.72% of reference with a coverageData >= 6X There is a 0.65% of reference with a coverageData >= 7X There is a 0.6% of reference with a coverageData >= 8X There is a 0.55% of reference with a coverageData >= 9X There is a 0.51% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.44% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.35% of reference with a coverageData >= 16X There is a 0.33% of reference with a coverageData >= 17X There is a 0.32% of reference with a coverageData >= 18X There is a 0.3% of reference with a coverageData >= 19X There is a 0.29% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% 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 0.15% 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 0.14% of reference with a coverageData >= 41X There is a 0.14% of reference with a coverageData >= 42X There is a 0.13% of reference with a coverageData >= 43X There is a 0.13% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.12% of reference with a coverageData >= 49X There is a 0.11% of reference with a coverageData >= 50X There is a 0.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 69088162 0.2771835100061797 9.26166734870909 chr2 243199373 100136158 0.4117451322541033 47.14061164001037 chr3 198022430 55722213 0.281393441136946 5.9940441968085745 chr4 191154276 65711115 0.3437595871514797 5.854877342954333 chr5 180915260 56750290 0.31368437355699014 5.593066262223173 chr6 171115067 62418742 0.36477642263962645 6.68812265066476 chr7 159138663 62536299 0.39296735200043753 7.469621408954914 chr8 146364022 60665399 0.4144830004739826 67.09836520800486 chr9 141213431 99373458 0.7037110938831307 143.0724964569612 chr10 135534747 37975730 0.28019183892378535 5.201009007353291 chr11 135006516 36748200 0.27219575090731174 18.08815239096504 chr12 133851895 32430223 0.24228437707213635 4.6741989921395986 chr13 115169878 53563311 0.4650809042274057 7.232635787795894 chr14 107349540 37372991 0.34814300089222555 6.321234870755232 chr15 102531392 7312036 0.07131509538073959 3.2285340715923754 chr16 90354753 17871535 0.19779297055905848 4.914741527876675 chr17 81195210 16025904 0.19737499293369645 4.706389040916823 chr18 78077248 8781618 0.11247345705627329 2.855202239018524 chr19 59128983 8235731 0.13928416458642626 33.6876321853472 chr20 63025520 15933166 0.25280499074025886 11.088221161100329 chr21 48129895 16025459 0.33296268358782 16.79127857242175 chr22 51304566 2122933 0.041379026576309014 1.7953017397077111 chrMT 16571 36611673 2209.3822340232937 2433.749150008588 chrX 155270560 32241464 0.20764698729752762 5.219168034021442 chrY 59373566 13299174 0.2239914981694042 19.46672876694921