BamQC report ----------------------------------- >>>>>>> Input bam file = SRR053623.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 = 12,755,729 number of mapped reads = 10,131,576 (79.43%) number of supplementary alignments = 317 (0%) number of secondary alignments = 0 number of mapped bases = 479,261,911 bp number of sequenced bases = 479,169,562 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,331,923 duplication rate = 16.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1596 >>>>>>> ACTG content number of A's = 141,041,627 bp (29.43%) number of C's = 91,350,627 bp (19.06%) number of T's = 144,327,502 bp (30.12%) number of G's = 102,250,379 bp (21.34%) number of N's = 199,427 bp (0.04%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 2,618,747 number of insertions = 20,816 mapped reads with insertion percentage = 0.21% number of deletions = 62,336 mapped reads with deletion percentage = 0.61% homopolymer indels = 48.75% >>>>>>> Coverage mean coverageData = 0.1548X std coverageData = 1.0176X There is a 6.7% of reference with a coverageData >= 1X There is a 2.98% of reference with a coverageData >= 2X There is a 1.69% of reference with a coverageData >= 3X There is a 1.07% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.5% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.16% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 38041828 0.15262480730188432 1.0709527784012736 chr2 243199373 40803938 0.16777978288620013 1.2821489456297601 chr3 198022430 32764534 0.16545870081485214 0.9457587911170058 chr4 191154276 31475211 0.1646586812423699 0.9978991682114708 chr5 180915260 29760938 0.16450208788357598 0.9261001651286238 chr6 171115067 28613319 0.1672168295968934 1.0055606856118717 chr7 159138663 25734540 0.16171142521160933 1.1914753542865852 chr8 146364022 24385195 0.16660648338838352 1.0321539864040015 chr9 141213431 19929567 0.14113081779027095 0.9938401559494898 chr10 135534747 22198974 0.1637880653586198 1.0344808015021847 chr11 135006516 21610325 0.1600687554962162 1.0607076434540332 chr12 133851895 21907251 0.16366784347730004 0.9385529987349559 chr13 115169878 15676042 0.13611234354177226 0.848313327903264 chr14 107349540 14585165 0.13586611549523175 0.9862673563862429 chr15 102531392 13803275 0.13462486688954736 0.8285328476333993 chr16 90354753 13270555 0.14687168698253206 0.9210955464046238 chr17 81195210 12282964 0.1512769534064879 0.880744183773146 chr18 78077248 12562008 0.16089204373596774 1.09160734074815 chr19 59128983 8473592 0.14330691261847003 1.0092538827624575 chr20 63025520 10141401 0.1609094379546571 0.9635338655267068 chr21 48129895 6277011 0.13041813201545527 0.9446737516195965 chr22 51304566 5232449 0.10198797900366217 0.7170927755941667 chrMT 16571 91747 5.5366000844849435 12.558881903787535 chrX 155270560 28480672 0.18342609184896352 1.1242919203403958 chrY 59373566 1159410 0.01952737688014225 0.37443994361803307