BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085015.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 = 1,896,266 number of mapped reads = 1,732,679 (91.37%) number of supplementary alignments = 12,301 (0.65%) number of secondary alignments = 0 number of mapped bases = 116,049,206 bp number of sequenced bases = 116,009,791 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,636 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6526 >>>>>>> ACTG content number of A's = 32,843,348 bp (28.31%) number of C's = 22,367,705 bp (19.28%) number of T's = 35,496,947 bp (30.6%) number of G's = 25,289,090 bp (21.8%) number of N's = 12,701 bp (0.01%) GC percentage = 41.08% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 982,931 number of insertions = 8,016 mapped reads with insertion percentage = 0.46% number of deletions = 22,575 mapped reads with deletion percentage = 1.29% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.2736X There is a 3.27% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% 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 9817552 0.039388274984478375 0.3413779207585523 chr2 243199373 10996839 0.045217382201063486 0.3306636787661526 chr3 198022430 7184459 0.0362810364462248 0.21186117379058755 chr4 191154276 6783361 0.03548631577564082 0.2121465055160417 chr5 180915260 5791489 0.03201216414801051 0.1983141515682832 chr6 171115067 7835032 0.04578808948483771 0.2836801835044697 chr7 159138663 10127742 0.06364098961922283 0.32646058374367337 chr8 146364022 6861540 0.046879963438009375 0.4902294640534794 chr9 141213431 3717506 0.02632544208914519 0.2369932240841201 chr10 135534747 9448800 0.06971496394205097 0.3541646419771586 chr11 135006516 4520058 0.03348029512886622 0.25554886652538544 chr12 133851895 4677934 0.03494858253594393 0.21012441549970443 chr13 115169878 3414877 0.029650782472826792 0.19121007836810353 chr14 107349540 3809600 0.035487809263085805 0.21654696969143775 chr15 102531392 1948516 0.019004091937033295 0.15776250468976274 chr16 90354753 2924867 0.032370925744216246 0.20654277412124297 chr17 81195210 1838168 0.022638872416242288 0.1779050283930965 chr18 78077248 2622113 0.033583573539887064 0.35674618880948333 chr19 59128983 1670263 0.028247788398457655 0.25783042389713096 chr20 63025520 2659369 0.04219511397922619 0.2292231087604649 chr21 48129895 1263127 0.02624412540272527 0.18676248991671418 chr22 51304566 730730 0.014242981803997717 0.13056237797864198 chrMT 16571 6537 0.39448434011224426 0.6552054463589486 chrX 155270560 5174199 0.033323760795349745 0.21453949406378373 chrY 59373566 224528 0.0037816155425126393 0.07915532256939765