BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975238.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 53,164,990 number of mapped reads = 53,022,591 (99.73%) number of supplementary alignments = 113,601 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 26,503,233 number of mapped paired reads (second in pair) = 26,519,358 number of mapped paired reads (both in pair) = 52,947,902 number of mapped paired reads (singletons) = 74,689 number of mapped bases = 4,875,654,212 bp number of sequenced bases = 4,873,997,582 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,271,080 duplication rate = 40.2% >>>>>>> Insert size mean insert size = 45,538.1073 std insert size = 2,080,924.0606 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 55.7499 >>>>>>> ACTG content number of A's = 1,278,553,062 bp (26.23%) number of C's = 1,078,902,229 bp (22.14%) number of T's = 1,334,894,883 bp (27.39%) number of G's = 1,181,450,328 bp (24.24%) number of N's = 197,080 bp (0%) GC percentage = 46.38% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 29,119,553 number of insertions = 478,966 mapped reads with insertion percentage = 0.89% number of deletions = 1,093,126 mapped reads with deletion percentage = 2.03% homopolymer indels = 45.77% >>>>>>> Coverage mean coverageData = 1.575X std coverageData = 22.5762X There is a 14.04% of reference with a coverageData >= 1X There is a 7.07% of reference with a coverageData >= 2X There is a 4.05% of reference with a coverageData >= 3X There is a 2.99% of reference with a coverageData >= 4X There is a 2.37% of reference with a coverageData >= 5X There is a 2.06% of reference with a coverageData >= 6X There is a 1.85% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.62% of reference with a coverageData >= 9X There is a 1.54% of reference with a coverageData >= 10X There is a 1.47% of reference with a coverageData >= 11X There is a 1.41% of reference with a coverageData >= 12X There is a 1.36% of reference with a coverageData >= 13X There is a 1.31% of reference with a coverageData >= 14X There is a 1.27% of reference with a coverageData >= 15X There is a 1.23% of reference with a coverageData >= 16X There is a 1.2% of reference with a coverageData >= 17X There is a 1.16% of reference with a coverageData >= 18X There is a 1.13% of reference with a coverageData >= 19X There is a 1.1% of reference with a coverageData >= 20X There is a 1.08% of reference with a coverageData >= 21X There is a 1.05% of reference with a coverageData >= 22X There is a 1.02% of reference with a coverageData >= 23X There is a 1% of reference with a coverageData >= 24X There is a 0.98% of reference with a coverageData >= 25X There is a 0.96% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.92% of reference with a coverageData >= 28X There is a 0.9% of reference with a coverageData >= 29X There is a 0.88% of reference with a coverageData >= 30X There is a 0.86% of reference with a coverageData >= 31X There is a 0.85% of reference with a coverageData >= 32X There is a 0.83% of reference with a coverageData >= 33X There is a 0.82% of reference with a coverageData >= 34X There is a 0.8% of reference with a coverageData >= 35X There is a 0.79% of reference with a coverageData >= 36X There is a 0.77% of reference with a coverageData >= 37X There is a 0.76% of reference with a coverageData >= 38X There is a 0.75% of reference with a coverageData >= 39X There is a 0.74% of reference with a coverageData >= 40X There is a 0.72% of reference with a coverageData >= 41X There is a 0.71% of reference with a coverageData >= 42X There is a 0.7% of reference with a coverageData >= 43X There is a 0.69% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.67% of reference with a coverageData >= 46X There is a 0.66% of reference with a coverageData >= 47X There is a 0.65% of reference with a coverageData >= 48X There is a 0.64% of reference with a coverageData >= 49X There is a 0.63% of reference with a coverageData >= 50X There is a 0.62% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 446585738 1.7917136423102433 22.51623277987116 chr2 243199373 398665090 1.6392521291574218 21.533183996823727 chr3 198022430 272073277 1.3739518144484946 19.502775144385215 chr4 191154276 144843757 0.757732236133708 11.819473756357892 chr5 180915260 195432541 1.0802435405393662 15.61138451142011 chr6 171115067 256737661 1.5003802149111745 21.963705858270313 chr7 159138663 204951635 1.2878808401199149 18.899466767336246 chr8 146364022 174738158 1.193860045742662 17.983910169306643 chr9 141213431 193450898 1.36991854549586 18.037834094840473 chr10 135534747 189564973 1.3986448286947406 19.183468318178974 chr11 135006516 378500009 2.8035684514664463 31.632097744156653 chr12 133851895 384166569 2.8700868896925216 35.03613535475325 chr13 115169878 70725565 0.6140977678208533 12.749939357820422 chr14 107349540 173439901 1.6156557447754318 22.16766269745455 chr15 102531392 141273444 1.3778555157039125 18.711330344366644 chr16 90354753 116139347 1.2853706434237058 17.405524305354582 chr17 81195210 292884934 3.607170102768378 37.276900545333774 chr18 78077248 99643321 1.276214563812495 19.90279432494057 chr19 59128983 243179884 4.112701955316904 45.54211327286001 chr20 63025520 289412134 4.591983279154222 50.062987614650346 chr21 48129895 33953332 0.7054520272691225 16.611942881871204 chr22 51304566 77462707 1.509859902138145 19.931867524098333 chrMT 16571 73593 4.4410717518556515 5.24210854785024 chrX 155270560 87654219 0.564525683426401 9.74806681606663 chrY 59373566 10101525 0.17013505639866738 3.4964708257845674