BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926967.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 = 33,496,372 number of mapped reads = 32,472,733 (96.94%) number of supplementary alignments = 1,110,898 (3.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,234,410 number of mapped paired reads (second in pair) = 16,238,323 number of mapped paired reads (both in pair) = 31,865,762 number of mapped paired reads (singletons) = 606,971 number of mapped bases = 2,865,131,520 bp number of sequenced bases = 2,862,830,679 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,434,106 duplication rate = 10.81% >>>>>>> Insert size mean insert size = 336,323.7252 std insert size = 5,699,448.1611 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 52.5063 >>>>>>> ACTG content number of A's = 814,594,647 bp (28.45%) number of C's = 547,945,453 bp (19.14%) number of T's = 846,388,794 bp (29.56%) number of G's = 653,578,244 bp (22.83%) number of N's = 323,541 bp (0.01%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 29,557,898 number of insertions = 507,718 mapped reads with insertion percentage = 1.54% number of deletions = 1,557,250 mapped reads with deletion percentage = 4.67% homopolymer indels = 51.66% >>>>>>> Coverage mean coverageData = 0.9255X std coverageData = 3.5231X There is a 34.84% of reference with a coverageData >= 1X There is a 19.88% of reference with a coverageData >= 2X There is a 11.62% of reference with a coverageData >= 3X There is a 7.36% of reference with a coverageData >= 4X There is a 4.83% of reference with a coverageData >= 5X There is a 3.29% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 1.65% of reference with a coverageData >= 8X There is a 1.21% of reference with a coverageData >= 9X There is a 0.9% of reference with a coverageData >= 10X There is a 0.69% of reference with a coverageData >= 11X There is a 0.53% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 239287420 0.9600273774242672 3.4671157430854365 chr2 243199373 255638895 1.0511494821987062 7.683500441875689 chr3 198022430 196240613 0.991001943567706 2.0554535308129394 chr4 191154276 172877156 0.9043855027339278 2.891391017695668 chr5 180915260 179010696 0.989472618285489 2.0319873983580528 chr6 171115067 165471450 0.9670185852190327 2.789957824589919 chr7 159138663 147082890 0.9242435950338479 2.5329263717723225 chr8 146364022 154298162 1.0542082671108888 2.455398611420779 chr9 141213431 126674831 0.8970452038659127 3.5497393758456397 chr10 135534747 133345289 0.9838457808904162 4.762436916599239 chr11 135006516 131640461 0.9750674626697278 3.9129109109501097 chr12 133851895 127050602 0.9491879214709661 2.188202339547449 chr13 115169878 91280971 0.7925767794943744 1.8529343256863278 chr14 107349540 82492304 0.7684458079652693 1.8789458697036636 chr15 102531392 80695237 0.7870295665155896 1.8968714032332858 chr16 90354753 83245847 0.9213222795263466 4.285348352995978 chr17 81195210 68348050 0.8417744100914327 2.2791783447734164 chr18 78077248 75545867 0.9675785063530927 3.697785782078885 chr19 59128983 42965408 0.726638711171474 2.4125959396466343 chr20 63025520 68500216 1.0868647493904056 2.364098135286797 chr21 48129895 34502796 0.7168682998373465 2.6230632024599547 chr22 51304566 31883074 0.6214471047274818 1.7819004010864956 chrMT 16571 614104 37.05895842133848 34.748728681091514 chrX 155270560 171225226 1.1027539670108744 2.468164202552239 chrY 59373566 5213955 0.08781609984483667 3.040532921797572