BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081961.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,672,757 number of mapped reads = 2,460,087 (92.04%) number of supplementary alignments = 15,363 (0.57%) number of secondary alignments = 0 number of mapped bases = 171,618,097 bp number of sequenced bases = 171,552,035 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,863 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1022 >>>>>>> ACTG content number of A's = 49,960,203 bp (29.12%) number of C's = 32,028,009 bp (18.67%) number of T's = 54,204,664 bp (31.6%) number of G's = 35,336,914 bp (20.6%) number of N's = 22,245 bp (0.01%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,324,340 number of insertions = 12,696 mapped reads with insertion percentage = 0.51% number of deletions = 37,554 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.0554X std coverageData = 0.5024X There is a 4.7% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 15834619 0.06352890490892699 0.9244890912520618 chr2 243199373 15146872 0.06228170662265647 0.6113189000856926 chr3 198022430 10915270 0.05512138195657936 0.2679220497399592 chr4 191154276 8961739 0.0468822313972197 0.2620638265459667 chr5 180915260 8818562 0.048744157900223566 0.2523080627318694 chr6 171115067 15022386 0.08779113530662966 0.4698862179041648 chr7 159138663 11174523 0.07021878146607277 0.664505644898454 chr8 146364022 10000607 0.06832694854477284 0.8059579062226526 chr9 141213431 8444520 0.05979969426562549 0.5216404293293969 chr10 135534747 6903314 0.05093390553198878 0.48487421422819904 chr11 135006516 7683064 0.05690883838525246 0.35788862830702384 chr12 133851895 7328339 0.05474960963384194 0.27850950929345236 chr13 115169878 4645813 0.0403387854591632 0.22514107740099426 chr14 107349540 4119372 0.0383734480837086 0.2471900209177635 chr15 102531392 3800756 0.03706919340371386 0.21775738439471548 chr16 90354753 3648256 0.040377023663602955 0.2847872831248612 chr17 81195210 4445788 0.05475431370889982 0.29891949164491477 chr18 78077248 4939132 0.06325955545974161 0.8361346373628097 chr19 59128983 3384066 0.057231933111381264 0.6271278939450264 chr20 63025520 4230016 0.0671159238352972 0.29898864662204977 chr21 48129895 1841813 0.03826754660487001 0.25659127422856004 chr22 51304566 1314859 0.02562849864084222 0.17791526545380346 chrMT 16571 10484 0.6326715346086537 0.8589452582988042 chrX 155270560 8628821 0.05557280787806781 0.3122679070057473 chrY 59373566 375106 0.006317727319932241 0.15996374323227802