BamQC report ----------------------------------- >>>>>>> Input bam file = SRR536763.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 = 22,948,608 number of mapped reads = 22,381,330 (97.53%) number of supplementary alignments = 550 (0%) number of secondary alignments = 0 number of mapped bases = 1,116,542,096 bp number of sequenced bases = 1,116,439,968 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 248,709 duplication rate = 1.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3349 >>>>>>> ACTG content number of A's = 339,236,108 bp (30.39%) number of C's = 217,270,141 bp (19.46%) number of T's = 337,612,816 bp (30.24%) number of G's = 222,281,713 bp (19.91%) number of N's = 39,190 bp (0%) GC percentage = 39.37% >>>>>>> Mismatches and indels general error rate = 0.0022 number of mismatches = 2,317,689 number of insertions = 68,296 mapped reads with insertion percentage = 0.3% number of deletions = 60,483 mapped reads with deletion percentage = 0.27% homopolymer indels = 48.68% >>>>>>> Coverage mean coverageData = 0.3607X std coverageData = 0.7086X There is a 26.3% of reference with a coverageData >= 1X There is a 7.11% of reference with a coverageData >= 2X There is a 1.9% of reference with a coverageData >= 3X There is a 0.52% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 83875529 0.33651081254477594 0.6973414555838765 chr2 243199373 105997325 0.4358453876441532 0.7685716116201396 chr3 198022430 83836836 0.4233704030396961 0.7492302516044295 chr4 191154276 93418708 0.48870843987816415 0.8137392805845342 chr5 180915260 75076012 0.41497888016743306 0.740277581891496 chr6 171115067 73742271 0.4309513609342186 0.7562570719428143 chr7 159138663 61111530 0.38401434854332034 0.7253012889813265 chr8 146364022 65364720 0.4465900779906144 0.7761562320149302 chr9 141213431 43669885 0.30924739021460357 0.6557290068230737 chr10 135534747 49293710 0.36369795267334654 0.6941985989237778 chr11 135006516 53254766 0.39446070884460127 0.7426702290423031 chr12 133851895 54485416 0.4070574869335993 0.7465058320293438 chr13 115169878 40682594 0.3532398810043022 0.6972640437245577 chr14 107349540 35136856 0.3273125902542293 0.6792767008274169 chr15 102531392 28638930 0.27931865003841944 0.6288315124913647 chr16 90354753 21370333 0.23651586984029496 0.5694456030379765 chr17 81195210 18496183 0.22779894281941016 0.5483828288705521 chr18 78077248 45723129 0.5856139934645237 0.9139285320548355 chr19 59128983 10057696 0.17009756450571795 0.46591940242722296 chr20 63025520 18838391 0.29890100073747905 0.6398962279356664 chr21 48129895 11567565 0.24034054094653645 0.5944968473332032 chr22 51304566 6824922 0.13302757497256676 0.4265073354196483 chrMT 16571 2371 0.14308128658499789 0.4055729594938882 chrX 155270560 31130546 0.20049226331121625 0.5098700204238031 chrY 59373566 4945872 0.0833009086905779 0.3406203311495759