BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708585.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 5,283,920 number of mapped reads = 5,190,226 (98.23%) number of supplementary alignments = 140 (0%) number of secondary alignments = 0 number of mapped bases = 258,902,722 bp number of sequenced bases = 258,880,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,742 duplication rate = 0.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7417 >>>>>>> ACTG content number of A's = 80,150,463 bp (30.96%) number of C's = 49,127,959 bp (18.98%) number of T's = 79,817,692 bp (30.83%) number of G's = 49,778,392 bp (19.23%) number of N's = 5,790 bp (0%) GC percentage = 38.21% >>>>>>> Mismatches and indels general error rate = 0.0015 number of mismatches = 375,527 number of insertions = 16,017 mapped reads with insertion percentage = 0.31% number of deletions = 13,196 mapped reads with deletion percentage = 0.25% homopolymer indels = 48.32% >>>>>>> Coverage mean coverageData = 0.0836X std coverageData = 0.3016X There is a 7.71% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0% 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 20692392 0.08301841703335215 0.3025030377129451 chr2 243199373 22411635 0.09215334202362438 0.31536203817620095 chr3 198022430 18947262 0.09568240325098526 0.3207216624442082 chr4 191154276 20652218 0.10803952928575869 0.3405731384644072 chr5 180915260 17659723 0.09761323063626584 0.32357048269284416 chr6 171115067 16802995 0.09819705122752283 0.32520970836508273 chr7 159138663 13909622 0.08740567337806526 0.3074012286761444 chr8 146364022 14540378 0.09934393576585372 0.32690935032535484 chr9 141213431 10509935 0.07442588800211221 0.28509856244734944 chr10 135534747 10834647 0.07993999501839923 0.2932166877301894 chr11 135006516 12146988 0.08997334617538015 0.31329045328683885 chr12 133851895 12460281 0.09309006047318194 0.3177872072009412 chr13 115169878 10279677 0.08925664573509404 0.3117495420080558 chr14 107349540 8434873 0.07857390911968509 0.2941980753947934 chr15 102531392 7112496 0.06936895970358034 0.27547767939032225 chr16 90354753 4867815 0.05387447631006196 0.242300214278656 chr17 81195210 4263993 0.05251532695093713 0.238661294117259 chr18 78077248 7033309 0.09008141526709548 0.31120466911076433 chr19 59128983 2155397 0.0364524619001142 0.197258751271243 chr20 63025520 4228991 0.0670996605819357 0.27029210279322524 chr21 48129895 3246216 0.06744697863978302 0.2728243360713135 chr22 51304566 1382633 0.026949511667246146 0.17008046358462697 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 13978515 0.0900268215687507 0.3118146490251046 chrY 59373566 350581 0.005904664712239114 0.08111205994146552