BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081110.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 = 2,460,553 number of mapped reads = 2,248,839 (91.4%) number of supplementary alignments = 23,180 (0.94%) number of secondary alignments = 0 number of mapped bases = 152,521,499 bp number of sequenced bases = 152,469,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,506 duplication rate = 3.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6892 >>>>>>> ACTG content number of A's = 43,150,087 bp (28.3%) number of C's = 28,823,563 bp (18.9%) number of T's = 47,703,358 bp (31.29%) number of G's = 32,790,514 bp (21.51%) number of N's = 1,626 bp (0%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 1,372,908 number of insertions = 11,912 mapped reads with insertion percentage = 0.53% number of deletions = 31,639 mapped reads with deletion percentage = 1.39% homopolymer indels = 46.07% >>>>>>> Coverage mean coverageData = 0.0493X std coverageData = 0.5803X There is a 4.16% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12994763 0.052135328481287914 1.0962153850270622 chr2 243199373 7725437 0.03176585903451322 0.5570932298257179 chr3 198022430 13392070 0.06762905596098381 0.29531984832851405 chr4 191154276 8305392 0.04344863308210798 0.2666185368254892 chr5 180915260 8984527 0.049661521090039615 0.2600787036982402 chr6 171115067 13070993 0.07638715414814991 0.7306716130852691 chr7 159138663 7952466 0.049971929197369216 0.6148919018579639 chr8 146364022 12262732 0.08378242024532505 0.8002712302240814 chr9 141213431 8176309 0.05790036359926699 0.7095218847210487 chr10 135534747 7042595 0.05196154606759254 0.44456416380617597 chr11 135006516 7223674 0.05350611373454004 0.48638470646651244 chr12 133851895 8120757 0.060669720066346466 0.3305055932879904 chr13 115169878 3537971 0.030719586244590796 0.19851822673798938 chr14 107349540 4388850 0.04088373364245436 0.3582770937677331 chr15 102531392 3968204 0.038702332257422194 0.22127972068335516 chr16 90354753 3839510 0.0424937247075425 0.41536526400956947 chr17 81195210 3224383 0.03971149283313634 0.26443750432211166 chr18 78077248 4002100 0.0512582103303641 1.2778202130060803 chr19 59128983 3052338 0.05162168948517176 0.7606723685903053 chr20 63025520 2334689 0.03704354997785024 0.256653445696017 chr21 48129895 2818825 0.058567029909373375 0.3589573470749415 chr22 51304566 1236090 0.024093177203759992 0.17171522595227937 chrMT 16571 66520 4.014241747631404 3.1057141480618373 chrX 155270560 4429296 0.028526309172839978 0.2953535887108616 chrY 59373566 371008 0.006248706705607004 0.1651612664422052