BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504647.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 150,537,108 number of mapped reads = 149,808,962 (99.52%) number of supplementary alignments = 1,694,717 (1.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 75,004,121 number of mapped paired reads (second in pair) = 74,804,841 number of mapped paired reads (both in pair) = 149,551,368 number of mapped paired reads (singletons) = 257,594 number of mapped bases = 13,871,683,269 bp number of sequenced bases = 13,868,369,982 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,601,596 duplication rate = 30.71% >>>>>>> Insert size mean insert size = 20,959.7571 std insert size = 1,357,714.3506 median insert size = 139 >>>>>>> Mapping quality mean mapping quality = 53.1331 >>>>>>> ACTG content number of A's = 4,084,030,166 bp (29.45%) number of C's = 2,825,015,964 bp (20.37%) number of T's = 4,152,688,752 bp (29.94%) number of G's = 2,795,238,915 bp (20.16%) number of N's = 11,396,185 bp (0.08%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 67,835,774 number of insertions = 1,386,544 mapped reads with insertion percentage = 0.92% number of deletions = 1,785,919 mapped reads with deletion percentage = 1.17% homopolymer indels = 50.27% >>>>>>> Coverage mean coverageData = 4.481X std coverageData = 656.2253X There is a 36.84% of reference with a coverageData >= 1X There is a 28.17% of reference with a coverageData >= 2X There is a 20.82% of reference with a coverageData >= 3X There is a 17.06% of reference with a coverageData >= 4X There is a 14.21% of reference with a coverageData >= 5X There is a 12.2% of reference with a coverageData >= 6X There is a 10.61% of reference with a coverageData >= 7X There is a 9.37% of reference with a coverageData >= 8X There is a 8.36% of reference with a coverageData >= 9X There is a 7.52% of reference with a coverageData >= 10X There is a 6.82% of reference with a coverageData >= 11X There is a 6.22% of reference with a coverageData >= 12X There is a 5.7% of reference with a coverageData >= 13X There is a 5.25% of reference with a coverageData >= 14X There is a 4.86% of reference with a coverageData >= 15X There is a 4.51% of reference with a coverageData >= 16X There is a 4.2% of reference with a coverageData >= 17X There is a 3.93% of reference with a coverageData >= 18X There is a 3.68% of reference with a coverageData >= 19X There is a 3.46% of reference with a coverageData >= 20X There is a 3.26% of reference with a coverageData >= 21X There is a 3.07% of reference with a coverageData >= 22X There is a 2.91% of reference with a coverageData >= 23X There is a 2.75% of reference with a coverageData >= 24X There is a 2.61% of reference with a coverageData >= 25X There is a 2.48% of reference with a coverageData >= 26X There is a 2.36% of reference with a coverageData >= 27X There is a 2.25% of reference with a coverageData >= 28X There is a 2.15% of reference with a coverageData >= 29X There is a 2.05% of reference with a coverageData >= 30X There is a 1.97% of reference with a coverageData >= 31X There is a 1.88% of reference with a coverageData >= 32X There is a 1.8% of reference with a coverageData >= 33X There is a 1.73% of reference with a coverageData >= 34X There is a 1.66% of reference with a coverageData >= 35X There is a 1.6% of reference with a coverageData >= 36X There is a 1.54% of reference with a coverageData >= 37X There is a 1.48% of reference with a coverageData >= 38X There is a 1.43% of reference with a coverageData >= 39X There is a 1.38% of reference with a coverageData >= 40X There is a 1.33% of reference with a coverageData >= 41X There is a 1.28% of reference with a coverageData >= 42X There is a 1.24% of reference with a coverageData >= 43X There is a 1.2% of reference with a coverageData >= 44X There is a 1.16% of reference with a coverageData >= 45X There is a 1.13% of reference with a coverageData >= 46X There is a 1.09% of reference with a coverageData >= 47X There is a 1.06% of reference with a coverageData >= 48X There is a 1.03% of reference with a coverageData >= 49X There is a 1% of reference with a coverageData >= 50X There is a 0.97% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 766697156 3.0760090102242916 22.662227029661274 chr2 243199373 902947857 3.7127885893028187 17.642880440017667 chr3 198022430 869668479 4.391767533607178 80.95275937186489 chr4 191154276 882382862 4.616077026704859 45.43807880804574 chr5 180915260 766336309 4.235885402922893 29.10311927323832 chr6 171115067 764546798 4.468027342092558 43.182094646823344 chr7 159138663 498765712 3.1341579889985627 13.236892629446332 chr8 146364022 602310828 4.115156305283822 29.849064739943753 chr9 141213431 3495688085 24.754643097652657 3068.311340439572 chr10 135534747 528932216 3.9025580355419853 59.964188210990265 chr11 135006516 500542704 3.7075447825051646 20.82216240179016 chr12 133851895 463979179 3.466362422437127 16.297433965785856 chr13 115169878 341426600 2.9645477266199762 12.503173492533985 chr14 107349540 392519834 3.6564649834549825 49.473389677260634 chr15 102531392 291063206 2.8387716222559427 13.741654627708371 chr16 90354753 249758041 2.764193722050239 24.800907620251486 chr17 81195210 167423004 2.0619812917535407 9.295604655771381 chr18 78077248 250702443 3.210953887616531 13.722771483704305 chr19 59128983 119240202 2.0166117519728015 11.611583792441946 chr20 63025520 152521353 2.4199935676849633 9.980454716082638 chr21 48129895 99199985 2.06108874744065 9.339621190119953 chr22 51304566 79351823 1.546681498095121 7.965703414478779 chrMT 16571 6574 0.3967171564781848 1.3992371614046901 chrX 155270560 675117034 4.348004116169865 21.90464818792058 chrY 59373566 10554985 0.17777246190670104 2.0226186370762105