BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472783.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 = 16,482,296 number of mapped reads = 16,324,594 (99.04%) number of supplementary alignments = 73,378 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,187,966 number of mapped paired reads (second in pair) = 8,136,628 number of mapped paired reads (both in pair) = 16,235,414 number of mapped paired reads (singletons) = 89,180 number of mapped bases = 1,607,328,243 bp number of sequenced bases = 1,607,094,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,355,406 duplication rate = 46.53% >>>>>>> Insert size mean insert size = 32,004.0286 std insert size = 1,741,523.8258 median insert size = 232 >>>>>>> Mapping quality mean mapping quality = 55.0917 >>>>>>> ACTG content number of A's = 445,354,649 bp (27.71%) number of C's = 360,081,405 bp (22.41%) number of T's = 443,070,459 bp (27.57%) number of G's = 358,276,837 bp (22.29%) number of N's = 311,146 bp (0.02%) GC percentage = 44.7% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 9,559,217 number of insertions = 98,335 mapped reads with insertion percentage = 0.6% number of deletions = 90,507 mapped reads with deletion percentage = 0.55% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.5192X std coverageData = 18.3031X There is a 4.76% of reference with a coverageData >= 1X There is a 2.1% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.67% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.43% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 152105418 0.6102509088633323 17.539874085644215 chr2 243199373 90014267 0.37012540735456584 11.969686651367194 chr3 198022430 176712074 0.8923841304240131 23.131223200938948 chr4 191154276 76960700 0.4026104025002297 17.083215189462063 chr5 180915260 77170719 0.4265572677506585 15.33865357619671 chr6 171115067 123515191 0.7218253375665628 28.89015211218063 chr7 159138663 58125201 0.36524877050148397 12.921921598376871 chr8 146364022 80106902 0.5473127952168464 16.136712009506876 chr9 141213431 113090856 0.8008505649862725 23.05039078426715 chr10 135534747 37299698 0.27520395194303937 12.307410154271336 chr11 135006516 77737235 0.5758035782509935 18.557139917062273 chr12 133851895 98464000 0.7356190213070947 24.601100986385173 chr13 115169878 37458850 0.32524867309488686 14.563454625404315 chr14 107349540 41773662 0.3891368514480826 14.748836355829757 chr15 102531392 36690130 0.3578428936183759 10.729071249456995 chr16 90354753 54803346 0.6065352865277602 16.0064710818893 chr17 81195210 63730181 0.7849007472238818 21.000555292015196 chr18 78077248 24395843 0.3124577725895257 11.514366991007721 chr19 59128983 34952070 0.5911156970178228 14.083855956171814 chr20 63025520 28747713 0.4561281366659093 14.427887496892604 chr21 48129895 6873244 0.14280612912203527 5.004508939651132 chr22 51304566 12630207 0.24618095395251954 7.460601006311562 chrMT 16571 4177 0.2520668637982017 0.6821126714650777 chrX 155270560 100284601 0.6458700284200688 29.15296841455325 chrY 59373566 3681958 0.062013421932581914 3.6517273091957323