BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3087917.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 = 1,621,739 number of mapped reads = 1,436,769 (88.59%) number of supplementary alignments = 12,768 (0.79%) number of secondary alignments = 0 number of mapped bases = 95,193,782 bp number of sequenced bases = 95,160,424 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,145 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3306 >>>>>>> ACTG content number of A's = 25,313,391 bp (26.6%) number of C's = 17,972,779 bp (18.89%) number of T's = 29,695,352 bp (31.21%) number of G's = 22,174,473 bp (23.3%) number of N's = 4,429 bp (0%) GC percentage = 42.19% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 640,167 number of insertions = 6,646 mapped reads with insertion percentage = 0.46% number of deletions = 19,909 mapped reads with deletion percentage = 1.37% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0308X std coverageData = 0.2497X There is a 2.55% of reference with a coverageData >= 1X There is a 0.4% 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% 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 7259660 0.02912594548761425 0.317776862367177 chr2 243199373 9948115 0.040905183583676424 0.38574973287053965 chr3 198022430 9332451 0.04712825208740242 0.26011623428503183 chr4 191154276 4781584 0.02501426648703375 0.1877313194247529 chr5 180915260 3751754 0.02073763152981125 0.16809345491267574 chr6 171115067 6438151 0.03762468795339922 0.25337808969191794 chr7 159138663 6755356 0.042449495758299795 0.3376731661359816 chr8 146364022 6483252 0.04429539385027285 0.27411488220559604 chr9 141213431 3254887 0.023049415179211954 0.20095851273010426 chr10 135534747 4017556 0.029642258453472452 0.21602817448963066 chr11 135006516 4011405 0.02971267697923558 0.22716692961924728 chr12 133851895 3454798 0.02581060208374338 0.18841573057352828 chr13 115169878 2777408 0.02411575012695594 0.1810896398226165 chr14 107349540 2469638 0.023005575990358226 0.17853780577859313 chr15 102531392 2441341 0.023810668638927675 0.1880436911710177 chr16 90354753 2652975 0.02936176473195605 0.20708542253299256 chr17 81195210 1712184 0.021087253792434306 0.17209729792518616 chr18 78077248 2713546 0.03475463172062622 0.3194797763600392 chr19 59128983 2444092 0.04133492368708591 0.29073040686563584 chr20 63025520 2169417 0.03442124713925407 0.22182098095990072 chr21 48129895 1372394 0.028514377602527494 0.20411555741442267 chr22 51304566 657657 0.012818683623597947 0.13100353036281956 chrMT 16571 7855 0.47402087985034097 1.269195478222981 chrX 155270560 4097466 0.026389200889080325 0.193253945970991 chrY 59373566 188840 0.003180539972956989 0.07348978132544325