BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819133.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,734,237 number of mapped reads = 3,426,384 (91.76%) number of supplementary alignments = 15,403 (0.41%) number of secondary alignments = 0 number of mapped bases = 200,389,480 bp number of sequenced bases = 200,329,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 405,709 duplication rate = 8.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.843 >>>>>>> ACTG content number of A's = 47,711,917 bp (23.82%) number of C's = 38,005,815 bp (18.97%) number of T's = 63,898,593 bp (31.9%) number of G's = 50,710,847 bp (25.31%) number of N's = 2,753 bp (0%) GC percentage = 44.29% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,033,968 number of insertions = 12,648 mapped reads with insertion percentage = 0.37% number of deletions = 35,430 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0647X std coverageData = 0.5804X There is a 4.62% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 19827861 0.07954989608631707 1.1669619843837973 chr2 243199373 15709170 0.06459379317560987 0.7092943508304974 chr3 198022430 10853380 0.05480884160445865 0.312955767375336 chr4 191154276 11621531 0.06079660493705095 0.4439253665822846 chr5 180915260 10443929 0.05772829224024552 0.3217136999047959 chr6 171115067 8782113 0.05132285048867146 0.396977949562144 chr7 159138663 9957128 0.06256888057429513 0.6755419271390924 chr8 146364022 18022530 0.12313497370275873 0.6245907633930009 chr9 141213431 7676541 0.05436126681179498 0.4287516506551904 chr10 135534747 10613483 0.07830820682463073 0.6425578839989686 chr11 135006516 7036949 0.052123032343120386 0.4762752894081061 chr12 133851895 9376888 0.07005420431290868 0.3620696309225661 chr13 115169878 4309151 0.03741560792484299 0.2624151713056513 chr14 107349540 4752349 0.044269859004519255 0.2907714422336155 chr15 102531392 5336019 0.052042783150744704 0.30507621327119444 chr16 90354753 6443355 0.07131174383266811 0.3941196218524273 chr17 81195210 7149685 0.08805550228886655 0.43228233473500693 chr18 78077248 4698098 0.06017243333166661 0.8926805317386294 chr19 59128983 4330670 0.0732410702886603 0.7821150639627058 chr20 63025520 5822550 0.09238400571704922 0.4286026391481829 chr21 48129895 2846787 0.059147999387906415 0.40537184973393864 chr22 51304566 1674756 0.03264341033505673 0.24015395440319545 chrMT 16571 183857 11.095105907911412 7.1151103719073205 chrX 155270560 12146800 0.07822989754142705 0.42174989425553444 chrY 59373566 773900 0.013034420064983128 0.41178380809658427