BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156419.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,202,508 number of mapped reads = 2,157,994 (97.98%) number of supplementary alignments = 296,039 (13.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,079,006 number of mapped paired reads (second in pair) = 1,078,988 number of mapped paired reads (both in pair) = 2,130,808 number of mapped paired reads (singletons) = 27,186 number of mapped bases = 242,575,895 bp number of sequenced bases = 242,404,568 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,634,301 duplication rate = 60.21% >>>>>>> Insert size mean insert size = 960,049.6751 std insert size = 8,979,869.7931 median insert size = 144 >>>>>>> Mapping quality mean mapping quality = 52.5052 >>>>>>> ACTG content number of A's = 72,464,674 bp (29.89%) number of C's = 48,121,406 bp (19.85%) number of T's = 71,915,416 bp (29.67%) number of G's = 49,901,127 bp (20.59%) number of N's = 1,945 bp (0%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 2,047,738 number of insertions = 26,851 mapped reads with insertion percentage = 1.2% number of deletions = 72,041 mapped reads with deletion percentage = 3.26% homopolymer indels = 41.19% >>>>>>> Coverage mean coverageData = 0.0784X std coverageData = 1.5981X There is a 1.97% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.94% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.28% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 20447708 0.08203673843604987 0.9391699916476255 chr2 243199373 21871754 0.08993343087278437 4.8535735384125696 chr3 198022430 17490318 0.08832493369564245 0.8494019208202125 chr4 191154276 16436549 0.08598577726819985 0.961937144114437 chr5 180915260 13676416 0.07559570154557443 0.7750656746418423 chr6 171115067 14316910 0.08366831893301366 0.8690377124298118 chr7 159138663 12332405 0.07749471289701611 0.8686194523405799 chr8 146364022 12957475 0.08852909904320612 1.0904854278345775 chr9 141213431 9827545 0.06959355728705438 0.8294516270420109 chr10 135534747 11247099 0.08298314084726922 1.1492736278959155 chr11 135006516 11296657 0.08367490203213598 0.8256541850936548 chr12 133851895 11381040 0.08502711149513423 0.8339503398898295 chr13 115169878 8367166 0.0726506456835875 0.7703096519904217 chr14 107349540 7727856 0.07198778867613219 0.7620954766775068 chr15 102531392 6999779 0.06826961834283884 0.7405303322870296 chr16 90354753 7383795 0.08172005074265434 0.8776584123280895 chr17 81195210 6790877 0.08363642387278757 0.8330494902626022 chr18 78077248 6509076 0.08336712892339648 1.0627502296956328 chr19 59128983 4538299 0.07675252929684247 0.8184688752231256 chr20 63025520 5448376 0.08644714077725975 0.8351075453870292 chr21 48129895 3674611 0.07634778758607307 0.8764116452538651 chr22 51304566 3096946 0.06036394499468137 0.8158585986127489 chrMT 16571 327088 19.738579446020157 19.44357246364014 chrX 155270560 6575684 0.0423498440399777 0.5785943591973299 chrY 59373566 1854466 0.031233865926126116 0.620987392925863