BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926897.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,515,742 number of mapped reads = 21,255,882 (90.39%) number of supplementary alignments = 556,387 (2.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,688,967 number of mapped paired reads (second in pair) = 10,566,915 number of mapped paired reads (both in pair) = 20,859,846 number of mapped paired reads (singletons) = 396,036 number of mapped bases = 1,910,255,269 bp number of sequenced bases = 1,908,768,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,817,578 duplication rate = 6.95% >>>>>>> Insert size mean insert size = 303,765.0363 std insert size = 5,423,955.9622 median insert size = 181 >>>>>>> Mapping quality mean mapping quality = 52.3939 >>>>>>> ACTG content number of A's = 538,701,280 bp (28.22%) number of C's = 373,284,456 bp (19.56%) number of T's = 547,469,556 bp (28.68%) number of G's = 449,158,821 bp (23.53%) number of N's = 154,702 bp (0.01%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 19,792,910 number of insertions = 324,395 mapped reads with insertion percentage = 1.5% number of deletions = 1,017,063 mapped reads with deletion percentage = 4.66% homopolymer indels = 51.77% >>>>>>> Coverage mean coverageData = 0.6171X std coverageData = 2.0821X There is a 28.12% of reference with a coverageData >= 1X There is a 13.96% of reference with a coverageData >= 2X There is a 7.31% of reference with a coverageData >= 3X There is a 4.21% of reference with a coverageData >= 4X There is a 2.53% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.03% of reference with a coverageData >= 7X There is a 0.68% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.16% of reference with a coverageData >= 12X There is a 0.12% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% 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 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 159582979 0.6402510788528788 1.861855975134309 chr2 243199373 159132853 0.6543308522427811 2.8472801756995696 chr3 198022430 129355338 0.6532357874812464 1.4584978167467568 chr4 191154276 114152657 0.597175534802057 1.5140854240509911 chr5 180915260 116461358 0.6437342985881899 1.4281930248677257 chr6 171115067 110984942 0.6485983025679439 1.4399011618138007 chr7 159138663 99553712 0.6255784114511507 1.6363498607177331 chr8 146364022 97815318 0.6683016540772567 1.5926179295411864 chr9 141213431 82276736 0.5826410095509966 2.4823130697464975 chr10 135534747 91685389 0.6764714660219199 5.056932249655656 chr11 135006516 87064722 0.6448927398437568 1.745730346139337 chr12 133851895 87734756 0.6554614411697347 1.5469575190914457 chr13 115169878 57482558 0.499111043601175 1.2581925705110029 chr14 107349540 58440493 0.5443944426776305 1.3555363608641977 chr15 102531392 58182418 0.5674595542407149 1.446455457519218 chr16 90354753 61406229 0.6796126043308425 3.145356456438241 chr17 81195210 51580338 0.635263311715063 1.5536203143660523 chr18 78077248 49986577 0.6402195041505562 2.39795488148027 chr19 59128983 29872707 0.505212595995436 1.4312380980487776 chr20 63025520 45772712 0.7262567924865991 1.635204986084619 chr21 48129895 24511962 0.5092876682984661 1.7618470962783546 chr22 51304566 25002171 0.48732837931033274 1.3529728808040988 chrMT 16571 10722 0.6470339750165952 0.9740051780911896 chrX 155270560 109412823 0.7046591639780265 1.5747335488671816 chrY 59373566 2792799 0.0470377507727934 0.9766897831954852