BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1505991.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 10,961,598 number of mapped reads = 5,305,907 (48.4%) number of supplementary alignments = 196 (0%) number of secondary alignments = 0 number of mapped bases = 246,009,569 bp number of sequenced bases = 245,959,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 348,302 duplication rate = 4.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3171 >>>>>>> ACTG content number of A's = 70,740,075 bp (28.76%) number of C's = 51,614,012 bp (20.98%) number of T's = 70,322,588 bp (28.59%) number of G's = 52,508,531 bp (21.35%) number of N's = 774,404 bp (0.31%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,938,026 number of insertions = 10,870 mapped reads with insertion percentage = 0.2% number of deletions = 35,416 mapped reads with deletion percentage = 0.67% homopolymer indels = 43.77% >>>>>>> Coverage mean coverageData = 0.0795X std coverageData = 0.6589X There is a 5.9% of reference with a coverageData >= 1X There is a 1.32% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% 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% 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 23765119 0.09534627799382694 1.0046113584920173 chr2 243199373 14959303 0.06151045052241973 0.48694451489314633 chr3 198022430 14532029 0.07338577251072012 0.34972746974456276 chr4 191154276 10145773 0.0530763591184327 0.3225516852552735 chr5 180915260 17645335 0.09753370168995142 0.40415378421202575 chr6 171115067 16654497 0.09732922583608608 0.4884195557750882 chr7 159138663 16122497 0.10131099945209418 0.8839655082666297 chr8 146364022 14170744 0.09681849273040612 0.7487450536747846 chr9 141213431 11706703 0.08290077591840396 0.46998254020902785 chr10 135534747 7783983 0.057431641496331565 0.7096597662481244 chr11 135006516 12388703 0.09176374124045983 0.5062103194104531 chr12 133851895 7075614 0.052861515333794865 0.3141117158548694 chr13 115169878 7492097 0.0650525739030478 0.32723340918784 chr14 107349540 8717456 0.08120627251872714 1.871420637160195 chr15 102531392 8186288 0.07984177177658916 0.36387970572017236 chr16 90354753 7771257 0.08600828115815888 0.45483712917135005 chr17 81195210 4576507 0.05636424858067366 0.34207761570668893 chr18 78077248 7651960 0.09800499115952448 0.7180048197343931 chr19 59128983 6222632 0.10523827206701661 0.7977286814328218 chr20 63025520 5872964 0.09318390391701648 0.42105731953142694 chr21 48129895 3623528 0.07528643060617522 0.39579860809778983 chr22 51304566 1818949 0.03545393990858436 0.24956490919043334 chrMT 16571 53397 3.222316094381751 3.0267382199820383 chrX 155270560 16248971 0.10464940037570548 0.452554846759117 chrY 59373566 823263 0.01386581698663678 0.24332435204876826