BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926983.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 17,447,094 number of mapped reads = 17,138,564 (98.23%) number of supplementary alignments = 326,225 (1.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,604,566 number of mapped paired reads (second in pair) = 8,533,998 number of mapped paired reads (both in pair) = 16,954,024 number of mapped paired reads (singletons) = 184,540 number of mapped bases = 1,603,378,023 bp number of sequenced bases = 1,602,158,325 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,061,433 duplication rate = 4.86% >>>>>>> Insert size mean insert size = 194,714.8095 std insert size = 4,367,736.4378 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.1005 >>>>>>> ACTG content number of A's = 461,271,250 bp (28.79%) number of C's = 315,874,239 bp (19.72%) number of T's = 468,590,144 bp (29.25%) number of G's = 356,293,919 bp (22.24%) number of N's = 128,773 bp (0.01%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 14,874,741 number of insertions = 272,829 mapped reads with insertion percentage = 1.56% number of deletions = 842,457 mapped reads with deletion percentage = 4.79% homopolymer indels = 52.48% >>>>>>> Coverage mean coverageData = 0.5179X std coverageData = 2.0963X There is a 25.69% of reference with a coverageData >= 1X There is a 12.26% of reference with a coverageData >= 2X There is a 5.86% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 1.67% of reference with a coverageData >= 5X There is a 0.94% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 134563174 0.5398709678641082 2.550112978148981 chr2 243199373 149393236 0.614282981724628 3.6023880733384637 chr3 198022430 105427826 0.5324034555075402 1.1834397743135276 chr4 191154276 101161402 0.5292133878292108 1.9251921725029149 chr5 180915260 94558141 0.5226653683055813 1.1660951192487576 chr6 171115067 93884131 0.5486608084605431 1.4996539212604227 chr7 159138663 85075679 0.5346009410673508 1.7702719110851146 chr8 146364022 87497825 0.5978096516096012 1.4772961597846093 chr9 141213431 66922229 0.4739083848192882 2.852985362741961 chr10 135534747 73691846 0.5437118350174808 2.921335140352065 chr11 135006516 82095627 0.6080864052517287 1.9460079590385055 chr12 133851895 69465766 0.5189748415590232 1.3993142463199224 chr13 115169878 45953140 0.3990031143386294 1.0823437243632195 chr14 107349540 46089677 0.42934210058096195 1.1186717563675517 chr15 102531392 44809580 0.43703278699269 1.1523992037840012 chr16 90354753 48777387 0.5398430672484933 3.292538834629177 chr17 81195210 39134639 0.4819821144621709 1.940916778777601 chr18 78077248 40229140 0.5152479247219369 2.838031756461362 chr19 59128983 24273446 0.41051688644805545 1.6385456366569133 chr20 63025520 35875494 0.5692217057471323 1.3581711607051306 chr21 48129895 18986951 0.39449392108584486 1.5935884216213916 chr22 51304566 18157656 0.3539189085041671 1.034486738210275 chrMT 16571 219624 13.25351517711665 11.938234060435471 chrX 155270560 94291450 0.6072719129756472 1.471315883017754 chrY 59373566 2842957 0.047882537491516004 1.7126218663219215