BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549121.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 11,437,455 number of mapped reads = 6,794,963 (59.41%) number of secondary alignments = 0 number of mapped bases = 269,860,588 bp number of sequenced bases = 269,835,141 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 249,749 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9905 >>>>>>> ACTG content number of A's = 79,153,535 bp (29.33%) number of C's = 55,757,790 bp (20.66%) number of T's = 79,362,063 bp (29.41%) number of G's = 55,550,961 bp (20.59%) number of N's = 10,792 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 824,643 number of insertions = 6,591 mapped reads with insertion percentage = 0.1% number of deletions = 20,204 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.0872X std coverageData = 0.5646X There is a 7% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.25% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 22143414 0.08883995518711266 1.0703400054348602 chr2 243199373 23518274 0.09670367859048716 0.51660979748885 chr3 198022430 17201278 0.08686530106715688 0.35342530748181566 chr4 191154276 17886723 0.09357218354874781 0.3948171853584621 chr5 180915260 17085647 0.09444005442105878 0.376656249141577 chr6 171115067 16049244 0.09379211475281718 0.4019749566906802 chr7 159138663 15299717 0.09614079138015631 0.8168928080116925 chr8 146364022 14056486 0.09603785006673293 0.6221794675720991 chr9 141213431 11572694 0.08195179394798502 0.48297049166974815 chr10 135534747 13069739 0.0964309100750378 0.534847391117744 chr11 135006516 12658189 0.09375983748814021 0.4959378602498838 chr12 133851895 12487628 0.09329436837633116 0.38273812652350236 chr13 115169878 8830224 0.07667129768080505 0.32765867681591737 chr14 107349540 8457396 0.07878371905459493 0.44460037149397524 chr15 102531392 8156310 0.0795493930288199 0.33297765291240894 chr16 90354753 7642899 0.08458768073883174 0.37951257313116693 chr17 81195210 7222585 0.08895333850358907 0.37853552389448314 chr18 78077248 7287526 0.09333738299792534 0.9729017427931318 chr19 59128983 5194737 0.08785432687046216 0.8743654957082576 chr20 63025520 5756974 0.091343538300041 0.3859603712895097 chr21 48129895 3615545 0.07512056695739727 0.38084565284712685 chr22 51304566 3160037 0.06159367959569135 0.3060930764222693 chrMT 16571 99394 5.998068915575403 7.536169419046263 chrX 155270560 9047645 0.05827018979000269 0.35609604141321827 chrY 59373566 2360283 0.03975309483685046 0.40052452191099