BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068930.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 = 1,758,841 number of mapped reads = 1,379,552 (78.44%) number of supplementary alignments = 4,683 (0.27%) number of secondary alignments = 0 number of mapped bases = 85,481,148 bp number of sequenced bases = 85,441,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,261 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3487 >>>>>>> ACTG content number of A's = 21,791,755 bp (25.51%) number of C's = 14,082,322 bp (16.48%) number of T's = 28,804,151 bp (33.71%) number of G's = 20,568,285 bp (24.07%) number of N's = 194,593 bp (0.23%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 839,005 number of insertions = 7,272 mapped reads with insertion percentage = 0.52% number of deletions = 25,808 mapped reads with deletion percentage = 1.85% homopolymer indels = 48.9% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.4287X There is a 2.36% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 10575867 0.042430654565951915 0.7279338515890381 chr2 243199373 8894606 0.036573309751090514 0.4304993082240139 chr3 198022430 4563464 0.02304518735579601 0.208444149235085 chr4 191154276 4292864 0.02245758813158854 0.18395335751473907 chr5 180915260 5146694 0.028448092217317655 0.19228380630077874 chr6 171115067 4086171 0.023879668059855887 0.21536178957730812 chr7 159138663 8175374 0.05137264474818417 1.081713170017531 chr8 146364022 3861907 0.026385630479599693 0.2947333585287173 chr9 141213431 4572736 0.03238173570048022 0.40220430538327 chr10 135534747 3064609 0.022611242266900016 0.5496881747862029 chr11 135006516 4435445 0.032853562416202194 0.451911698350536 chr12 133851895 3166466 0.023656489883837655 0.18579884249159828 chr13 115169878 1881846 0.01633974119517605 0.1425684144339081 chr14 107349540 2268572 0.021132573087877228 0.20180420382387437 chr15 102531392 1729966 0.01687254962850792 0.14820122591080437 chr16 90354753 1661333 0.01838678038331863 0.20422912606675922 chr17 81195210 2199243 0.02708587119855962 0.23943282454351034 chr18 78077248 1669987 0.021388907047543478 0.5364105129701782 chr19 59128983 1437603 0.024313000614267288 0.42359850061392307 chr20 63025520 1213032 0.019246679757660073 0.17491825993847923 chr21 48129895 1195758 0.024844392450887334 0.1996781166123759 chr22 51304566 749753 0.014613767515351362 0.13366929949619089 chrMT 16571 84556 5.102649206444994 3.966004987719393 chrX 155270560 4328681 0.027878311252306942 0.2591067782743782 chrY 59373566 224615 0.0037830808410598076 0.10249358389189046