BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975219.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 4,116,172 number of mapped reads = 4,072,849 (98.95%) number of supplementary alignments = 48,247 (1.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,045,208 number of mapped paired reads (second in pair) = 2,027,641 number of mapped paired reads (both in pair) = 4,052,432 number of mapped paired reads (singletons) = 20,417 number of mapped bases = 582,877,346 bp number of sequenced bases = 582,459,100 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 519,958 duplication rate = 11.34% >>>>>>> Insert size mean insert size = 97,260.0116 std insert size = 3,085,770.4311 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 53.9471 >>>>>>> ACTG content number of A's = 171,364,335 bp (29.42%) number of C's = 118,725,242 bp (20.38%) number of T's = 169,734,003 bp (29.14%) number of G's = 122,582,018 bp (21.05%) number of N's = 53,502 bp (0.01%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 5,378,753 number of insertions = 101,656 mapped reads with insertion percentage = 2.38% number of deletions = 226,968 mapped reads with deletion percentage = 5.36% homopolymer indels = 48.85% >>>>>>> Coverage mean coverageData = 0.1883X std coverageData = 1.9598X There is a 10.04% of reference with a coverageData >= 1X There is a 5.76% of reference with a coverageData >= 2X There is a 1.29% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 62572722 0.25104339459198377 2.230787496580361 chr2 243199373 44113562 0.18138846928688424 1.717758238082792 chr3 198022430 38858667 0.19623366403492776 0.6816126832360926 chr4 191154276 29001874 0.15171972402019404 1.0771919634613518 chr5 180915260 39064245 0.21592564938966452 0.6764384613797009 chr6 171115067 37150352 0.21710742748328526 0.9667880221998731 chr7 159138663 32892110 0.2066883645993683 1.7590040011728527 chr8 146364022 34786429 0.2376706278268303 0.8419749007954396 chr9 141213431 26253620 0.18591446871650616 2.266810464432407 chr10 135534747 24401224 0.180036666169451 5.82535158501148 chr11 135006516 21417700 0.15864197251042314 1.7502283623951065 chr12 133851895 30004910 0.22416499968117748 0.6913964968936223 chr13 115169878 9822592 0.08528785625699803 0.4044355528643038 chr14 107349540 19348750 0.1802406419254335 0.6265182272286369 chr15 102531392 9738796 0.09498355391488296 0.4338559494923856 chr16 90354753 22057290 0.244118757095158 4.209446487933932 chr17 81195210 17259841 0.2125721578896095 2.5130217383002496 chr18 78077248 17869254 0.2288663401660878 2.125648803662295 chr19 59128983 13504674 0.22839347668130872 1.4144804289104973 chr20 63025520 13733882 0.2179098561979338 0.7499162292786655 chr21 48129895 7988069 0.16596896793562504 0.8039128983576515 chr22 51304566 3434033 0.06693425688466013 0.37673212555850033 chrMT 16571 41465 2.5022629895600748 2.69751985567504 chrX 155270560 22441172 0.14452947165257857 0.7646494589922257 chrY 59373566 5120113 0.08623556483031523 1.5379375274592217