BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124832.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 = 29,321,452 number of mapped reads = 28,828,195 (98.32%) number of supplementary alignments = 304,584 (1.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,458,239 number of mapped paired reads (second in pair) = 14,369,956 number of mapped paired reads (both in pair) = 28,644,596 number of mapped paired reads (singletons) = 183,599 number of mapped bases = 2,468,465,358 bp number of sequenced bases = 2,466,800,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,832,772 duplication rate = 14.33% >>>>>>> Insert size mean insert size = 108,939.3902 std insert size = 3,127,452.4517 median insert size = 179 >>>>>>> Mapping quality mean mapping quality = 52.1207 >>>>>>> ACTG content number of A's = 698,862,937 bp (28.33%) number of C's = 455,856,323 bp (18.48%) number of T's = 743,757,605 bp (30.15%) number of G's = 568,300,995 bp (23.04%) number of N's = 22,165 bp (0%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 20,367,578 number of insertions = 405,107 mapped reads with insertion percentage = 1.35% number of deletions = 909,401 mapped reads with deletion percentage = 3.08% homopolymer indels = 45.42% >>>>>>> Coverage mean coverageData = 0.7974X std coverageData = 8.5978X There is a 27.26% of reference with a coverageData >= 1X There is a 15.39% of reference with a coverageData >= 2X There is a 9.34% of reference with a coverageData >= 3X There is a 6.15% of reference with a coverageData >= 4X There is a 4.21% of reference with a coverageData >= 5X There is a 2.99% of reference with a coverageData >= 6X There is a 2.18% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.24% of reference with a coverageData >= 9X There is a 0.96% of reference with a coverageData >= 10X There is a 0.75% of reference with a coverageData >= 11X There is a 0.6% of reference with a coverageData >= 12X There is a 0.48% of reference with a coverageData >= 13X There is a 0.39% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.22% of reference with a coverageData >= 17X There is a 0.19% of reference with a coverageData >= 18X There is a 0.16% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.12% of reference with a coverageData >= 21X There is a 0.1% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.07% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.04% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.03% of reference with a coverageData >= 36X There is a 0.03% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 175442607 0.7038803205228524 8.712402487592797 chr2 243199373 197477913 0.8120000909706293 17.24597555268243 chr3 198022430 210633973 1.063687446922048 2.511217937808431 chr4 191154276 126730648 0.662975742169639 5.381485880694152 chr5 180915260 139176425 0.7692906889114827 2.5676933368337567 chr6 171115067 168802640 0.9864861286586762 7.090876312954853 chr7 159138663 180444889 1.133884661328341 9.570620792226457 chr8 146364022 179805105 1.2284788470762302 4.799788135851433 chr9 141213431 83723072 0.5928832081135399 10.408601443257764 chr10 135534747 118024993 0.8708098521776116 14.969049461497486 chr11 135006516 143984545 1.0665007087509761 6.441742735131067 chr12 133851895 108199010 0.8083487349954963 2.152560235407203 chr13 115169878 51292046 0.4453599056517191 1.5117977703239116 chr14 107349540 74553182 0.6944899996776884 2.8488737940480866 chr15 102531392 47495911 0.46323287018282167 1.6735791117341274 chr16 90354753 71873430 0.7954582090440776 12.741238618888225 chr17 81195210 66121312 0.8143499105427524 7.163300970740771 chr18 78077248 39960033 0.5118012484251494 11.073484049898525 chr19 59128983 35301865 0.5970314929989579 5.7437966874399 chr20 63025520 60753254 0.9639468900851591 3.32210389044938 chr21 48129895 36626938 0.7610018264116304 4.0306974823280575 chr22 51304566 22216496 0.43303155512513253 2.1712060173521497 chrMT 16571 3658812 220.79608955404018 130.5348446057449 chrX 155270560 90700600 0.5841455070426744 4.006032199562739 chrY 59373566 35465659 0.5973307885869614 15.328526602690886