BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046482.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,931,742 number of mapped reads = 7,900,090 (99.6%) number of supplementary alignments = 36,133 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,954,145 number of mapped paired reads (second in pair) = 3,945,945 number of mapped paired reads (both in pair) = 7,879,392 number of mapped paired reads (singletons) = 20,698 number of mapped bases = 746,650,253 bp number of sequenced bases = 746,409,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,731,660 duplication rate = 38.98% >>>>>>> Insert size mean insert size = 15,322.7103 std insert size = 1,232,895.6589 median insert size = 116 >>>>>>> Mapping quality mean mapping quality = 51.599 >>>>>>> ACTG content number of A's = 217,338,906 bp (29.12%) number of C's = 156,045,159 bp (20.91%) number of T's = 214,228,445 bp (28.7%) number of G's = 158,740,341 bp (21.27%) number of N's = 56,346 bp (0.01%) GC percentage = 42.17% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 2,665,810 number of insertions = 70,505 mapped reads with insertion percentage = 0.88% number of deletions = 84,535 mapped reads with deletion percentage = 1.04% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.2412X std coverageData = 22.8569X There is a 2.55% of reference with a coverageData >= 1X There is a 1.71% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.13% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.08% of reference with a coverageData >= 8X There is a 0.07% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.05% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% 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 0.04% of reference with a coverageData >= 33X There is a 0.04% of reference with a coverageData >= 34X There is a 0.04% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 102111620 0.40967448582605537 28.693456153108293 chr2 243199373 110449460 0.4541519109919745 32.108267952027234 chr3 198022430 16444932 0.08304580445760613 7.070586981400967 chr4 191154276 21210479 0.11096000279899572 13.641558140298057 chr5 180915260 76964942 0.42541984573330077 43.792056697489265 chr6 171115067 56055781 0.32759114660545935 21.718927096484183 chr7 159138663 20704003 0.13010039552738983 9.242687806105456 chr8 146364022 63424345 0.43333289242352196 29.547805858185338 chr9 141213431 14141551 0.10014310182719093 20.046014184379324 chr10 135534747 16653202 0.12287035146787857 10.343981194369396 chr11 135006516 28874147 0.2138722474698925 16.367334103549904 chr12 133851895 33883587 0.25314237799920575 18.49118486441527 chr13 115169878 4444894 0.038594240761460216 3.4908497277586514 chr14 107349540 41220307 0.38398214840976497 21.707496942396055 chr15 102531392 5357888 0.0522560739251448 3.024912847794004 chr16 90354753 48814118 0.5402495870914505 44.86014261154718 chr17 81195210 34206739 0.4212901105865728 22.27383393509858 chr18 78077248 5531812 0.0708504992389076 2.41102110695175 chr19 59128983 1554541 0.026290677111764294 1.7606952810199015 chr20 63025520 11125752 0.17652773035430727 12.185934368574443 chr21 48129895 4248917 0.08828020505758427 10.723486320096006 chr22 51304566 5586053 0.1088802310500005 7.91101055629385 chrMT 16571 83254 5.024078208919196 3.616760557267217 chrX 155270560 23348160 0.1503708107963287 25.350616277864887 chrY 59373566 209769 0.003533036907367161 0.5862724669828848