BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819013.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 = 2,046,867 number of mapped reads = 1,995,911 (97.51%) number of supplementary alignments = 30,157 (1.47%) number of secondary alignments = 0 number of mapped bases = 184,798,804 bp number of sequenced bases = 184,689,414 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 851,192 duplication rate = 36.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1462 >>>>>>> ACTG content number of A's = 51,872,760 bp (28.09%) number of C's = 38,783,994 bp (21%) number of T's = 53,301,109 bp (28.86%) number of G's = 40,722,942 bp (22.05%) number of N's = 8,609 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,171,293 number of insertions = 29,844 mapped reads with insertion percentage = 1.46% number of deletions = 59,059 mapped reads with deletion percentage = 2.9% homopolymer indels = 41.53% >>>>>>> Coverage mean coverageData = 0.0597X std coverageData = 0.7005X There is a 2.84% of reference with a coverageData >= 1X There is a 1.35% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 19092980 0.07660153432476302 1.3038788884076693 chr2 243199373 15547678 0.06392976185839097 0.8966142244188872 chr3 198022430 9805499 0.04951711278363769 0.39519436528245366 chr4 191154276 10077256 0.05271792089024469 0.4719589682596309 chr5 180915260 10161637 0.05616793740892836 0.4365463431784102 chr6 171115067 7970365 0.04657897834326886 0.48029303910409266 chr7 159138663 8928154 0.05610298485415829 0.7886091859859246 chr8 146364022 16551087 0.11308166292396639 0.6987825968944876 chr9 141213431 7737254 0.05479120466947652 0.6449559959284508 chr10 135534747 9633312 0.0710763270174548 0.8244306061338837 chr11 135006516 6339811 0.046959296394257 0.4707382915802768 chr12 133851895 8436689 0.06303003031821103 0.4625217590808116 chr13 115169878 3803842 0.033028097850377164 0.32751394299907144 chr14 107349540 4117465 0.03835568368527709 0.3703609377395953 chr15 102531392 5014070 0.048902778965489904 0.39724940033764494 chr16 90354753 5899809 0.0652960558699109 0.6990718154987111 chr17 81195210 6248195 0.07695275374002974 0.5617846279104396 chr18 78077248 4142249 0.05305321468297653 0.7686073228206368 chr19 59128983 3866908 0.06539784389662173 1.2171993813876112 chr20 63025520 5017433 0.07960954546666175 0.5410616490761417 chr21 48129895 2667303 0.05541884103424701 0.46250300486925866 chr22 51304566 1517466 0.029577601338641086 0.37247560514052647 chrMT 16571 404433 24.406070846659826 17.112576062051307 chrX 155270560 11130147 0.07168227512028037 0.5693167564436115 chrY 59373566 687762 0.011583639763190238 0.6346784368317331