BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085144.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 = 1,793,435 number of mapped reads = 1,590,289 (88.67%) number of supplementary alignments = 13,528 (0.75%) number of secondary alignments = 0 number of mapped bases = 105,985,088 bp number of sequenced bases = 105,946,515 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,733 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6182 >>>>>>> ACTG content number of A's = 29,614,486 bp (27.95%) number of C's = 19,865,248 bp (18.75%) number of T's = 32,666,502 bp (30.83%) number of G's = 23,779,519 bp (22.44%) number of N's = 20,760 bp (0.02%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 949,335 number of insertions = 8,457 mapped reads with insertion percentage = 0.53% number of deletions = 23,664 mapped reads with deletion percentage = 1.47% homopolymer indels = 46.74% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.3341X There is a 3.08% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 8403871 0.0337165498977834 0.5877511714837103 chr2 243199373 9027993 0.03712177744800354 0.407830213861531 chr3 198022430 7147786 0.036095840254056065 0.20640591012842766 chr4 191154276 7041560 0.03683705197366341 0.21349724896424394 chr5 180915260 6583093 0.03638771544202518 0.20674515777472866 chr6 171115067 6176003 0.036092689605176614 0.2438266202696772 chr7 159138663 5975469 0.03754881992442025 0.4537791930429229 chr8 146364022 5487643 0.03749311425727287 0.5039196362487455 chr9 141213431 4428344 0.03135922672964443 0.3063593644473559 chr10 135534747 4982787 0.03676390822495135 0.31271188983077974 chr11 135006516 4778839 0.03539709890743348 0.2828749756945772 chr12 133851895 4750580 0.03549131672734256 0.20735804331582822 chr13 115169878 3425898 0.02974647589710914 0.18591253033476002 chr14 107349540 3189100 0.029707626134215386 0.20098518649549096 chr15 102531392 2959049 0.02885993199038983 0.19018978389352292 chr16 90354753 2911127 0.03221885848108068 0.22492185848021762 chr17 81195210 2685999 0.03308075685745501 0.2130053579257042 chr18 78077248 2845625 0.03644627689746442 0.5416591367427387 chr19 59128983 2085755 0.03527466386492729 0.4516946416644126 chr20 63025520 2069667 0.032838554921879266 0.20091636078265038 chr21 48129895 1392982 0.028942136690719978 0.19531387637600753 chr22 51304566 1095186 0.021346754984731767 0.156852578718373 chrMT 16571 2391 0.14428821435037112 0.3846683756003726 chrX 155270560 6262699 0.0403341045462836 0.24419582229347478 chrY 59373566 275642 0.004642503702742059 0.11143163874012092