BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536754.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP014781/SRP014781.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 = 21,888,688 number of mapped reads = 21,117,546 (96.48%) number of supplementary alignments = 500 (0%) number of secondary alignments = 0 number of mapped bases = 1,053,124,904 bp number of sequenced bases = 1,053,036,340 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,214 duplication rate = 0.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3857 >>>>>>> ACTG content number of A's = 324,037,479 bp (30.77%) number of C's = 200,652,487 bp (19.05%) number of T's = 324,232,506 bp (30.79%) number of G's = 203,690,678 bp (19.34%) number of N's = 423,190 bp (0.04%) GC percentage = 38.4% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,686,796 number of insertions = 55,842 mapped reads with insertion percentage = 0.26% number of deletions = 53,335 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.3402X std coverageData = 0.6446X There is a 26.44% of reference with a coverageData >= 1X There is a 6.06% of reference with a coverageData >= 2X There is a 1.22% of reference with a coverageData >= 3X There is a 0.23% of reference with a coverageData >= 4X There is a 0.04% 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 82958728 0.33283258299284235 0.6533689486863454 chr2 243199373 95501265 0.3926871349294145 0.6787825166862393 chr3 198022430 81408355 0.41110673674694326 0.6909160994609876 chr4 191154276 87384898 0.4571433076391134 0.727316719850695 chr5 180915260 74261679 0.4104776954691384 0.6902772271917486 chr6 171115067 70715982 0.4132656652613764 0.6958940668148978 chr7 159138663 59854395 0.376114728323437 0.6735108142920713 chr8 146364022 59647829 0.4075306771769363 0.6912059819363175 chr9 141213431 43909037 0.31094094017161866 0.6221542761179325 chr10 135534747 46010732 0.33947554423073517 0.6318573976669621 chr11 135006516 47853422 0.3544526843430283 0.659137378404511 chr12 133851895 49031811 0.3663139098628376 0.6678316023315463 chr13 115169878 43993266 0.38198586960385594 0.6840831210601066 chr14 107349540 34470461 0.32110487851182223 0.6364594332364295 chr15 102531392 27970811 0.2728024115775196 0.5851463204986399 chr16 90354753 19655103 0.21753258514247722 0.5175784545182607 chr17 81195210 16521179 0.20347479857494058 0.5010077815926701 chr18 78077248 31469057 0.403050284251822 0.6889272413275972 chr19 59128983 7378214 0.1247816827832131 0.3827819685130927 chr20 63025520 16181118 0.2567391431280535 0.5616022506340657 chr21 48129895 13851856 0.287801500501923 0.6209143997604458 chr22 51304566 5548384 0.10814600790112912 0.3644967545681955 chrMT 16571 4049 0.24434252609981294 0.496177964114702 chrX 155270560 32735034 0.21082576117455878 0.4818426408535062 chrY 59373566 4808239 0.08098282323146971 0.31775347344856764