BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084793.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 = 1,753,886 number of mapped reads = 1,568,104 (89.41%) number of supplementary alignments = 14,214 (0.81%) number of secondary alignments = 0 number of mapped bases = 105,763,970 bp number of sequenced bases = 105,722,530 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,540 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9117 >>>>>>> ACTG content number of A's = 29,396,463 bp (27.81%) number of C's = 19,957,438 bp (18.88%) number of T's = 32,914,342 bp (31.13%) number of G's = 23,403,127 bp (22.14%) number of N's = 51,160 bp (0.05%) GC percentage = 41.01% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 908,334 number of insertions = 7,987 mapped reads with insertion percentage = 0.5% number of deletions = 25,414 mapped reads with deletion percentage = 1.6% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.2744X There is a 3.01% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% 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 8097383 0.03248691203862637 0.4285468297956423 chr2 243199373 9548981 0.03926400336566657 0.31563431081487475 chr3 198022430 8395778 0.04239811621340067 0.22675010908629897 chr4 191154276 7566748 0.039584508169725696 0.22752927077915247 chr5 180915260 5513508 0.030475638152359288 0.1934237413149148 chr6 171115067 6314121 0.03689985406136095 0.23754047250908664 chr7 159138663 5563074 0.0349574006412257 0.3375351176393801 chr8 146364022 4926873 0.03366177652592794 0.35185855113698133 chr9 141213431 3517128 0.024906469413663635 0.22915816708506587 chr10 135534747 4961216 0.0366047534659138 0.283851368638204 chr11 135006516 5214355 0.038622987648981325 0.24038016150894148 chr12 133851895 5400534 0.04034708660643168 0.22387922768461746 chr13 115169878 3134344 0.027214963273643478 0.18291025812346984 chr14 107349540 2979017 0.02775062659793419 0.19268315701514896 chr15 102531392 3732862 0.0364070157167085 0.2151636662756146 chr16 90354753 3101921 0.034330468481276244 0.21646984571644842 chr17 81195210 2298281 0.028305622954851648 0.20236520584819784 chr18 78077248 2704606 0.034640129734080795 0.4287094303495061 chr19 59128983 2110156 0.035687337967575054 0.3552598781435559 chr20 63025520 1817655 0.028839984184184438 0.1936453164702668 chr21 48129895 1091546 0.022679168529247777 0.17470779065849923 chr22 51304566 1022084 0.019921891552498464 0.1550126831017035 chrMT 16571 4301 0.2595498159435158 0.535489313237715 chrX 155270560 6503344 0.04188394760732492 0.24904879252817513 chrY 59373566 244154 0.00411216668373936 0.10399997404175908