BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472676.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 = 15,341,216 number of mapped reads = 15,229,247 (99.27%) number of supplementary alignments = 92,518 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,634,368 number of mapped paired reads (second in pair) = 7,594,879 number of mapped paired reads (both in pair) = 15,156,832 number of mapped paired reads (singletons) = 72,415 number of mapped bases = 1,498,575,790 bp number of sequenced bases = 1,498,367,364 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,400,086 duplication rate = 49.43% >>>>>>> Insert size mean insert size = 21,017.5046 std insert size = 1,366,925.9961 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 54.6984 >>>>>>> ACTG content number of A's = 412,692,538 bp (27.54%) number of C's = 338,155,666 bp (22.57%) number of T's = 413,222,550 bp (27.58%) number of G's = 334,010,454 bp (22.29%) number of N's = 286,156 bp (0.02%) GC percentage = 44.86% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 8,688,134 number of insertions = 92,825 mapped reads with insertion percentage = 0.6% number of deletions = 78,062 mapped reads with deletion percentage = 0.51% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.4841X std coverageData = 23.3942X There is a 3.03% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.7% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.38% 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 0.3% 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 0.26% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% 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 0.17% 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 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% 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 0.15% of reference with a coverageData >= 44X There is a 0.15% 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 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 149505448 0.599819761331708 33.688040952378124 chr2 243199373 109736879 0.45122188287878523 24.47591316560552 chr3 198022430 131966244 0.6664206877978419 19.932042299668737 chr4 191154276 36886522 0.1929672868003225 11.004045478807255 chr5 180915260 65071412 0.35967895687738005 19.76796388996245 chr6 171115067 132684036 0.7754082578829835 24.952605936423502 chr7 159138663 98455624 0.6186782152367335 24.54202098623284 chr8 146364022 64077702 0.4377968104757329 18.599939042309224 chr9 141213431 142926998 1.012134589379108 43.73851859058273 chr10 135534747 30307553 0.22361463514592314 9.60795542680759 chr11 135006516 41028880 0.30390296124670013 12.879716997801783 chr12 133851895 47924102 0.3580382780535158 13.43093281232005 chr13 115169878 53190240 0.4618415936847654 26.50075439688888 chr14 107349540 26163494 0.24372246029186526 22.864740718190873 chr15 102531392 11256477 0.10978566447239885 7.750022071807185 chr16 90354753 105953472 1.172638610389428 48.63290350795966 chr17 81195210 38473988 0.4738455384252347 12.771064559201177 chr18 78077248 4274111 0.05474208056103617 2.4510567400866448 chr19 59128983 23505159 0.3975234784606392 15.943196019498656 chr20 63025520 71089373 1.1279458384476637 29.447175286888736 chr21 48129895 7769897 0.16143598484891772 8.503339872322867 chr22 51304566 11483426 0.22382853799016642 7.951946851088537 chrMT 16571 3817 0.2303421640214833 0.6132419216364423 chrX 155270560 93939723 0.6050066606316098 20.245410439189424 chrY 59373566 901213 0.015178690799875487 1.1316862199567284