BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926940.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 = 12,777,492 number of mapped reads = 12,504,977 (97.87%) number of supplementary alignments = 281,419 (2.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,252,427 number of mapped paired reads (second in pair) = 6,252,550 number of mapped paired reads (both in pair) = 12,339,724 number of mapped paired reads (singletons) = 165,253 number of mapped bases = 1,147,401,762 bp number of sequenced bases = 1,146,538,855 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 742,334 duplication rate = 4.72% >>>>>>> Insert size mean insert size = 236,723.95 std insert size = 4,856,631.9064 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.0504 >>>>>>> ACTG content number of A's = 320,058,102 bp (27.92%) number of C's = 232,913,620 bp (20.31%) number of T's = 326,925,040 bp (28.51%) number of G's = 266,594,884 bp (23.25%) number of N's = 47,209 bp (0%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 10,899,923 number of insertions = 198,064 mapped reads with insertion percentage = 1.55% number of deletions = 573,453 mapped reads with deletion percentage = 4.47% homopolymer indels = 51.18% >>>>>>> Coverage mean coverageData = 0.3706X std coverageData = 1.607X There is a 20.49% of reference with a coverageData >= 1X There is a 8.23% of reference with a coverageData >= 2X There is a 3.42% of reference with a coverageData >= 3X There is a 1.66% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.32% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.16% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.07% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% 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 0.02% 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 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 102417553 0.41090189701072 1.8298082129643094 chr2 243199373 99234406 0.4080372608526421 2.813111548287793 chr3 198022430 72167327 0.3644401646823544 0.9839645483964902 chr4 191154276 61901677 0.32383098246779474 1.406108635098392 chr5 180915260 65636932 0.3628048402329356 0.9718142950320543 chr6 171115067 64796873 0.37867426951946903 1.145907622997899 chr7 159138663 57710112 0.3626404225854279 1.1937024238169467 chr8 146364022 52985029 0.3620085610929713 1.0195412681036937 chr9 141213431 48768690 0.3453544726917654 1.691336113681249 chr10 135534747 53590387 0.39539961660163797 2.60045994368501 chr11 135006516 55042223 0.4077004920266219 1.3830496925984646 chr12 133851895 53764817 0.4016739322218785 1.1303008419502598 chr13 115169878 31830162 0.27637575512583246 0.8211415052155103 chr14 107349540 35804383 0.3335308469882591 0.9511718165061559 chr15 102531392 35109881 0.3424305504405909 0.9786678867139597 chr16 90354753 40346861 0.44653833539891363 2.7264409765177633 chr17 81195210 38263574 0.471254080136008 1.3762433787420427 chr18 78077248 27566268 0.3530640321749045 1.6367341896246455 chr19 59128983 27743866 0.4692092539457342 1.605679724303365 chr20 63025520 30623660 0.48589301603540913 1.3917966713584558 chr21 48129895 14138450 0.2937560948346137 1.3580839712819868 chr22 51304566 17848380 0.3478906731225443 1.058273979395733 chrMT 16571 866117 52.26703276808883 43.58320460981386 chrX 155270560 56059644 0.3610449012356238 1.057302097191571 chrY 59373566 3184490 0.05363481115484962 1.595370357507774