BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617384.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,400,271 (91.88%) number of supplementary alignments = 87,845 (0.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,858,312 number of mapped paired reads (second in pair) = 14,541,959 number of mapped paired reads (both in pair) = 28,705,782 number of mapped paired reads (singletons) = 694,489 number of mapped bases = 2,875,756,361 bp number of sequenced bases = 2,874,927,310 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,544,144 duplication rate = 1.51% >>>>>>> Insert size mean insert size = 56,098.3136 std insert size = 2,259,200.4188 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.3375 >>>>>>> ACTG content number of A's = 873,982,925 bp (30.4%) number of C's = 567,930,680 bp (19.75%) number of T's = 860,979,409 bp (29.95%) number of G's = 571,242,472 bp (19.87%) number of N's = 791,824 bp (0.03%) GC percentage = 39.62% >>>>>>> Mismatches and indels general error rate = 0.013 number of mismatches = 36,556,214 number of insertions = 289,173 mapped reads with insertion percentage = 0.95% number of deletions = 345,766 mapped reads with deletion percentage = 1.14% homopolymer indels = 41.1% >>>>>>> Coverage mean coverageData = 0.929X std coverageData = 9.5446X There is a 51.87% of reference with a coverageData >= 1X There is a 23.1% of reference with a coverageData >= 2X There is a 8.78% of reference with a coverageData >= 3X There is a 3.06% of reference with a coverageData >= 4X There is a 1.05% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.03% 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 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 0.02% 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 186023382 0.7463306661129643 19.44954035822912 chr2 243199373 284165965 1.1684485921762635 8.47334874437777 chr3 198022430 229442956 1.1586715504905176 1.4706430368115495 chr4 191154276 158096227 0.8270608971363005 8.762688019019262 chr5 180915260 181145140 1.0012706501375286 1.467027989352809 chr6 171115067 135280285 0.7905807908779886 3.610501767310655 chr7 159138663 233464156 1.467048620359466 10.818636123899342 chr8 146364022 121134307 0.8276235193919446 7.479568390983164 chr9 141213431 120961917 0.8565893211673329 14.306926592863856 chr10 135534747 121402862 0.8957323836668983 19.96162161460518 chr11 135006516 154002462 1.1407039198019153 5.432447512824349 chr12 133851895 126673557 0.9463710394238348 1.379558184548796 chr13 115169878 126110931 1.0949992583998396 1.3117991946541834 chr14 107349540 83313642 0.7760968700937144 1.3623896766414982 chr15 102531392 64572008 0.6297779318162383 1.0869066393725948 chr16 90354753 72147369 0.7984900252009985 7.922930981872459 chr17 81195210 88609389 1.0913130097206474 7.061902933424903 chr18 78077248 51865229 0.6642809567263437 14.691260803571618 chr19 59128983 52450567 0.8870534269124839 9.417602389303646 chr20 63025520 81724639 1.2966912292036623 2.3671892177583245 chr21 48129895 45855205 0.9527385214532464 3.076920587601727 chr22 51304566 25319942 0.4935221944962949 0.908381014702674 chrMT 16571 1894899 114.35031078389959 20.33099280969534 chrX 155270560 120393158 0.7753765942494185 2.9407098515873016 chrY 59373566 9706167 0.16347623452497362 7.842809816315741