BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926993.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 = 12,597,560 number of mapped reads = 12,256,848 (97.3%) number of supplementary alignments = 372,088 (2.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,148,105 number of mapped paired reads (second in pair) = 6,108,743 number of mapped paired reads (both in pair) = 12,049,792 number of mapped paired reads (singletons) = 207,056 number of mapped bases = 1,120,953,978 bp number of sequenced bases = 1,120,100,207 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 766,434 duplication rate = 5.16% >>>>>>> Insert size mean insert size = 306,825.9413 std insert size = 5,419,341.0254 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 52.5624 >>>>>>> ACTG content number of A's = 320,544,387 bp (28.62%) number of C's = 219,495,411 bp (19.6%) number of T's = 325,424,264 bp (29.05%) number of G's = 254,423,167 bp (22.71%) number of N's = 212,978 bp (0.02%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 10,953,748 number of insertions = 193,958 mapped reads with insertion percentage = 1.55% number of deletions = 577,938 mapped reads with deletion percentage = 4.59% homopolymer indels = 51.78% >>>>>>> Coverage mean coverageData = 0.3621X std coverageData = 1.4618X There is a 20.95% of reference with a coverageData >= 1X There is a 8.42% of reference with a coverageData >= 2X There is a 3.34% of reference with a coverageData >= 3X There is a 1.5% of reference with a coverageData >= 4X There is a 0.7% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 88980670 0.35699277154458925 1.8870463461983793 chr2 243199373 97798724 0.40213394793579504 2.496935141155998 chr3 198022430 76892550 0.38830222414703225 0.9118287835770281 chr4 191154276 67017826 0.3505954844557074 1.2304442561882225 chr5 180915260 69227615 0.38265215991177304 0.901906548280156 chr6 171115067 66771863 0.39021615203528515 1.0909408216111074 chr7 159138663 58876860 0.3699720664361746 1.2330990375513367 chr8 146364022 57894223 0.3955495497383913 1.0502359653491826 chr9 141213431 47266491 0.3347166814465403 1.6680074728312742 chr10 135534747 52535922 0.38761958215777687 2.425237516777632 chr11 135006516 51185266 0.3791318190893838 1.3105563943496148 chr12 133851895 51543238 0.38507664011779585 0.9297989820322505 chr13 115169878 34622503 0.3006211658920052 0.7988524242636991 chr14 107349540 33782043 0.31469201451631745 0.8379913285476158 chr15 102531392 33102530 0.3228526342449345 0.8527551872226931 chr16 90354753 35790158 0.3961070869177187 1.9970237018208226 chr17 81195210 27498005 0.33866535969301637 1.0368368782042088 chr18 78077248 30393088 0.38926945785794087 1.684317437513739 chr19 59128983 18519908 0.3132120165165026 1.3437485558405051 chr20 63025520 25122867 0.3986141962811255 0.9862468021389412 chr21 48129895 14566207 0.3026436479863503 1.2334835292138213 chr22 51304566 13868509 0.2703172462271682 0.815915377753056 chrMT 16571 148627 8.969102649206445 8.740186743048564 chrX 155270560 65341382 0.42082273677637283 1.03649728168798 chrY 59373566 2206903 0.03716979034070482 1.4119084611039805