BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617730.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 49,598,236 number of mapped reads = 48,658,923 (98.11%) number of supplementary alignments = 1,086,585 (2.19%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,605,726 number of mapped paired reads (second in pair) = 24,053,197 number of mapped paired reads (both in pair) = 48,018,940 number of mapped paired reads (singletons) = 639,983 number of mapped bases = 6,468,140,715 bp number of sequenced bases = 6,463,086,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,778,473 duplication rate = 25.69% >>>>>>> Insert size mean insert size = 143,483.8937 std insert size = 3,621,942.1865 median insert size = 268 >>>>>>> Mapping quality mean mapping quality = 53.3861 >>>>>>> ACTG content number of A's = 1,858,174,552 bp (28.75%) number of C's = 1,233,296,894 bp (19.08%) number of T's = 1,927,179,817 bp (29.82%) number of G's = 1,444,165,626 bp (22.34%) number of N's = 269,176 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 75,280,211 number of insertions = 1,140,797 mapped reads with insertion percentage = 2.21% number of deletions = 2,604,898 mapped reads with deletion percentage = 5.14% homopolymer indels = 45.97% >>>>>>> Coverage mean coverageData = 2.0894X std coverageData = 20.7841X There is a 43.49% of reference with a coverageData >= 1X There is a 31.86% of reference with a coverageData >= 2X There is a 23.73% of reference with a coverageData >= 3X There is a 18.36% of reference with a coverageData >= 4X There is a 14.33% of reference with a coverageData >= 5X There is a 11.4% of reference with a coverageData >= 6X There is a 9.14% of reference with a coverageData >= 7X There is a 7.41% of reference with a coverageData >= 8X There is a 6.05% of reference with a coverageData >= 9X There is a 4.98% of reference with a coverageData >= 10X There is a 4.12% of reference with a coverageData >= 11X There is a 3.44% of reference with a coverageData >= 12X There is a 2.88% of reference with a coverageData >= 13X There is a 2.42% of reference with a coverageData >= 14X There is a 2.05% of reference with a coverageData >= 15X There is a 1.74% of reference with a coverageData >= 16X There is a 1.49% of reference with a coverageData >= 17X There is a 1.27% of reference with a coverageData >= 18X There is a 1.1% of reference with a coverageData >= 19X There is a 0.95% of reference with a coverageData >= 20X There is a 0.82% of reference with a coverageData >= 21X There is a 0.71% of reference with a coverageData >= 22X There is a 0.62% of reference with a coverageData >= 23X There is a 0.54% of reference with a coverageData >= 24X There is a 0.48% of reference with a coverageData >= 25X There is a 0.42% of reference with a coverageData >= 26X There is a 0.37% of reference with a coverageData >= 27X There is a 0.33% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.16% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.13% of reference with a coverageData >= 37X There is a 0.12% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 568420999 2.2805198908611746 14.764270161394032 chr2 243199373 401939011 1.6527140100809388 24.71581215037525 chr3 198022430 511073749 2.5808881801925168 5.003853692209943 chr4 191154276 195194663 1.0211367858702778 23.4354243178487 chr5 180915260 519393102 2.8709192469446747 5.174262238459148 chr6 171115067 515621699 3.013303901520256 11.448163087082843 chr7 159138663 322546565 2.0268271639306157 20.68939052892423 chr8 146364022 355169257 2.4266158591897673 6.255783153908682 chr9 141213431 230195171 1.6301223571290469 37.537629298533055 chr10 135534747 374229851 2.7611358657717493 59.10254672022243 chr11 135006516 308350423 2.2839669679350885 18.40997070156161 chr12 133851895 281739200 2.1048577608856416 9.089448384411794 chr13 115169878 188823889 1.6395249546066204 3.5396014506643247 chr14 107349540 266250521 2.480220418271005 5.0258281233422695 chr15 102531392 249575160 2.4341341235277483 5.87972722243077 chr16 90354753 159438472 1.7645831204917355 19.59801647031047 chr17 81195210 117662623 1.4491325658250038 11.415924692613057 chr18 78077248 184281742 2.3602489421758306 30.624198209020246 chr19 59128983 95372798 1.6129619208908093 8.385675105537542 chr20 63025520 153684590 2.4384501706610275 7.9814100032510265 chr21 48129895 88798391 1.8449737112453706 11.841341473891784 chr22 51304566 73692097 1.4363652739991992 3.8088086069089435 chrMT 16571 2781354 167.84466839659646 90.5655217662262 chrX 155270560 248650707 1.6014027836313594 6.339068141791937 chrY 59373566 55254681 0.9306276298108825 27.354756303692838