BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053634.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 16,393,961 number of mapped reads = 11,859,734 (72.34%) number of supplementary alignments = 364 (0%) number of secondary alignments = 0 number of mapped bases = 557,711,616 bp number of sequenced bases = 557,585,967 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,335,511 duplication rate = 19.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8602 >>>>>>> ACTG content number of A's = 170,044,719 bp (30.5%) number of C's = 104,870,648 bp (18.81%) number of T's = 169,338,626 bp (30.37%) number of G's = 113,325,665 bp (20.32%) number of N's = 6,309 bp (0%) GC percentage = 39.13% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,668,130 number of insertions = 25,218 mapped reads with insertion percentage = 0.21% number of deletions = 84,589 mapped reads with deletion percentage = 0.71% homopolymer indels = 48.47% >>>>>>> Coverage mean coverageData = 0.1802X std coverageData = 1.2769X There is a 6.39% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 1.94% of reference with a coverageData >= 3X There is a 1.35% of reference with a coverageData >= 4X There is a 0.99% of reference with a coverageData >= 5X There is a 0.75% of reference with a coverageData >= 6X There is a 0.58% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 43571411 0.17480963868892427 1.3563152839486152 chr2 243199373 47595765 0.1957067751157401 1.387136283277603 chr3 198022430 38861450 0.1962477179984106 1.2418737427541355 chr4 191154276 37745433 0.1974605736781949 1.3333400298645928 chr5 180915260 35400363 0.19567372592007992 1.240513510849893 chr6 171115067 33685169 0.19685682617299854 1.3343918988483525 chr7 159138663 30352317 0.19072874201538315 1.4006230983289827 chr8 146364022 28775811 0.19660440186591757 1.4179581054306774 chr9 141213431 22918063 0.1622937905955985 1.1837379655356528 chr10 135534747 25331452 0.18690005744430985 1.3122549553979066 chr11 135006516 25055474 0.18558714603078863 1.3210779160302162 chr12 133851895 25606028 0.19130119898564008 1.2388123365004786 chr13 115169878 18631147 0.1617710057833004 1.1386794641387155 chr14 107349540 17112413 0.15940834958398517 1.2154548756690142 chr15 102531392 15942838 0.15549226133592334 1.1035119206846653 chr16 90354753 14856590 0.16442510777490588 1.174689837052777 chr17 81195210 13574074 0.16717826088509408 1.1135715541911844 chr18 78077248 14779145 0.18928875413231777 1.4219868148202315 chr19 59128983 9191596 0.15544992546210376 1.2125809392459002 chr20 63025520 11111279 0.17629809321684295 1.1716331078620135 chr21 48129895 7125002 0.1480369321395777 1.1271657792073455 chr22 51304566 5639759 0.1099270384628144 0.8844058805543071 chrMT 16571 29567 1.7842616619395328 3.7788236933345396 chrX 155270560 33447265 0.21541279299823482 1.4085194832986505 chrY 59373566 1372205 0.023111379228931608 0.4575991726492507