BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548956.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 = 8,409,934 number of mapped reads = 7,195,995 (85.57%) number of secondary alignments = 0 number of mapped bases = 284,433,570 bp number of sequenced bases = 284,407,350 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 360,039 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.9267 >>>>>>> ACTG content number of A's = 80,180,718 bp (28.19%) number of C's = 61,219,694 bp (21.53%) number of T's = 81,801,694 bp (28.76%) number of G's = 61,204,846 bp (21.52%) number of N's = 398 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 880,376 number of insertions = 9,285 mapped reads with insertion percentage = 0.13% number of deletions = 20,384 mapped reads with deletion percentage = 0.28% homopolymer indels = 39.65% >>>>>>> Coverage mean coverageData = 0.0919X std coverageData = 0.9046X There is a 7.46% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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% 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 22918629 0.09195013800988684 1.6884548004353837 chr2 243199373 24285594 0.09985878540895744 0.9183460099640007 chr3 198022430 19256705 0.09724506966205798 0.3723104792495434 chr4 191154276 19060457 0.0997124280913287 0.48187379649397594 chr5 180915260 17659184 0.09761025134087639 0.3900499968510611 chr6 171115067 16393320 0.09580290203199932 0.408539528449128 chr7 159138663 16409240 0.10311284316872764 1.3917412270746221 chr8 146364022 14738001 0.10069415146298727 1.4341773090269998 chr9 141213431 12148583 0.08602994002744682 0.8926015824766264 chr10 135534747 13763422 0.10154902934226896 0.8257563189863831 chr11 135006516 13052649 0.09668162238924824 0.6219032394880208 chr12 133851895 13152117 0.0982587284251747 0.4161387177598943 chr13 115169878 9011675 0.07824680512381892 0.3218765074264234 chr14 107349540 8732746 0.0813487044285425 0.5376735612556294 chr15 102531392 7957444 0.07760983094816463 0.33847617137485464 chr16 90354753 8106193 0.08971518078301868 0.48990661629039045 chr17 81195210 7639194 0.09408429388876512 0.4052306205671733 chr18 78077248 7605779 0.09741351283282935 1.7576625247559905 chr19 59128983 6333378 0.10711122834634243 1.7003643664468302 chr20 63025520 5726226 0.09085567243237343 0.412615582884475 chr21 48129895 3659878 0.07604167846200371 0.5539723483587341 chr22 51304566 3252566 0.06339720328206265 0.41404460463780673 chrMT 16571 11750 0.7090700621567799 1.1498871049890735 chrX 155270560 10642987 0.06854478402087298 0.5457745135766097 chrY 59373566 2915853 0.04911028924892266 0.5390774721588328