BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124926.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,213,594 number of mapped reads = 6,137,419 (98.77%) number of supplementary alignments = 35,196 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,070,932 number of mapped paired reads (second in pair) = 3,066,487 number of mapped paired reads (both in pair) = 6,113,650 number of mapped paired reads (singletons) = 23,769 number of mapped bases = 562,467,755 bp number of sequenced bases = 562,147,233 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 404,264 duplication rate = 3.28% >>>>>>> Insert size mean insert size = 80,438.0409 std insert size = 2,736,882.9911 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 52.5354 >>>>>>> ACTG content number of A's = 163,278,304 bp (29.05%) number of C's = 109,852,185 bp (19.54%) number of T's = 169,226,418 bp (30.1%) number of G's = 119,780,529 bp (21.31%) number of N's = 9,797 bp (0%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 4,439,204 number of insertions = 97,527 mapped reads with insertion percentage = 1.56% number of deletions = 187,974 mapped reads with deletion percentage = 3% homopolymer indels = 45.57% >>>>>>> Coverage mean coverageData = 0.1817X std coverageData = 2.2441X There is a 11.29% of reference with a coverageData >= 1X There is a 3.88% of reference with a coverageData >= 2X There is a 1.16% of reference with a coverageData >= 3X There is a 0.44% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% 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 48318599 0.19385548090570254 2.620949973876663 chr2 243199373 41801726 0.17188254017414756 2.36772621686074 chr3 198022430 54715478 0.2763094968585124 0.8720121912074623 chr4 191154276 35707616 0.1867999855781411 1.0966174141365936 chr5 180915260 33483354 0.1850775550940258 0.5962933469881706 chr6 171115067 32122716 0.1877258184400559 2.6435209718817014 chr7 159138663 32303067 0.20298691965257998 2.8656536109502104 chr8 146364022 37718454 0.25770304398986793 0.9702888565401512 chr9 141213431 21075325 0.14924447944331867 3.2807574027483484 chr10 135534747 27327861 0.20162992594068885 5.44687173312009 chr11 135006516 26467885 0.19604894477833945 1.8580353603867363 chr12 133851895 21294635 0.15909102370198047 0.5388946635552532 chr13 115169878 14738147 0.12796876454102 0.4877188934617347 chr14 107349540 20029452 0.18658162857521327 0.7108755726385088 chr15 102531392 10089877 0.09840768571639015 0.4147556534943228 chr16 90354753 16821155 0.18616790419425971 3.6718000217229942 chr17 81195210 10730580 0.13215779600791722 1.494761538649423 chr18 78077248 18727295 0.2398559821165828 3.660179157107916 chr19 59128983 11098051 0.18769223546428998 1.5461756863497578 chr20 63025520 12425159 0.19714488670621044 0.6585582180726571 chr21 48129895 6739142 0.14001987745869796 0.6755333338807676 chr22 51304566 4478806 0.08729838977684755 0.4143577260030267 chrMT 16571 147210 8.883591817029751 6.081961738048848 chrX 155270560 16433486 0.10583774541677443 0.8788321009647564 chrY 59373566 7672679 0.12922718840906405 2.9317978433660588