BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472507.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,773,196 number of mapped reads = 16,530,807 (98.55%) number of supplementary alignments = 60,180 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,294,628 number of mapped paired reads (second in pair) = 8,236,179 number of mapped paired reads (both in pair) = 16,415,120 number of mapped paired reads (singletons) = 115,687 number of mapped bases = 1,627,269,946 bp number of sequenced bases = 1,627,059,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,310,724 duplication rate = 45.95% >>>>>>> Insert size mean insert size = 26,112.1551 std insert size = 1,580,745.7716 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 55.042 >>>>>>> ACTG content number of A's = 460,480,346 bp (28.3%) number of C's = 355,724,721 bp (21.86%) number of T's = 457,605,896 bp (28.12%) number of G's = 352,997,266 bp (21.7%) number of N's = 250,998 bp (0.02%) GC percentage = 43.56% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,334,621 number of insertions = 94,439 mapped reads with insertion percentage = 0.57% number of deletions = 89,406 mapped reads with deletion percentage = 0.53% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.5257X std coverageData = 17.862X There is a 5.36% of reference with a coverageData >= 1X There is a 2.37% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.28% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.26% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.23% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192632005 0.7728446341563979 24.165216071739103 chr2 243199373 128280789 0.5274717093945798 19.524605839871995 chr3 198022430 187679399 0.9477683866418567 21.70152032496747 chr4 191154276 85885710 0.44930049066754857 18.494680694927556 chr5 180915260 62416090 0.34500179807938813 10.057419883896085 chr6 171115067 100089716 0.5849263758871683 18.12898661156072 chr7 159138663 65186587 0.4096213061686964 14.791196668831732 chr8 146364022 90365042 0.617399281361645 21.83416071548174 chr9 141213431 97412560 0.6898250351271473 17.65201738330406 chr10 135534747 52905993 0.3903500332649014 15.919536673074225 chr11 135006516 90171815 0.6679071327194311 23.92083479351723 chr12 133851895 84208511 0.6291170625563426 23.174074884599076 chr13 115169878 26736378 0.23214731546385767 8.111746347123898 chr14 107349540 38380980 0.3575327849565075 14.167207105273711 chr15 102531392 47264131 0.4609722942218516 16.227993119386614 chr16 90354753 46345506 0.5129282573546519 14.79874926015677 chr17 81195210 51227705 0.6309202845832901 17.372968511130118 chr18 78077248 29789769 0.38154225159165445 16.515218915364315 chr19 59128983 16615708 0.28100784348007474 7.836943146786703 chr20 63025520 39030739 0.6192846802374657 18.78289257064652 chr21 48129895 9144833 0.19000317785858456 8.207030174992637 chr22 51304566 11329208 0.22082260670521997 7.160819684010973 chrMT 16571 2836 0.1711423571299258 0.6046627642133571 chrX 155270560 71772460 0.46224126453849335 14.008990419459035 chrY 59373566 2395476 0.040345833362948086 1.4084500947633538