BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926937.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 16,630,356 number of mapped reads = 16,330,632 (98.2%) number of supplementary alignments = 244,887 (1.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,156,938 number of mapped paired reads (second in pair) = 8,173,694 number of mapped paired reads (both in pair) = 16,156,798 number of mapped paired reads (singletons) = 173,834 number of mapped bases = 1,530,768,957 bp number of sequenced bases = 1,529,648,375 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 963,075 duplication rate = 4.58% >>>>>>> Insert size mean insert size = 123,577.1702 std insert size = 3,483,320.2836 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.5032 >>>>>>> ACTG content number of A's = 428,096,573 bp (27.99%) number of C's = 315,896,113 bp (20.65%) number of T's = 434,188,064 bp (28.38%) number of G's = 351,402,045 bp (22.97%) number of N's = 65,580 bp (0%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 14,196,174 number of insertions = 246,987 mapped reads with insertion percentage = 1.48% number of deletions = 768,158 mapped reads with deletion percentage = 4.58% homopolymer indels = 52.04% >>>>>>> Coverage mean coverageData = 0.4945X std coverageData = 2.1733X There is a 24.25% of reference with a coverageData >= 1X There is a 11.17% of reference with a coverageData >= 2X There is a 5.34% of reference with a coverageData >= 3X There is a 2.86% of reference with a coverageData >= 4X There is a 1.63% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.21% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 138061959 0.5539081846460073 2.6486969209298943 chr2 243199373 128904455 0.5300361321244031 3.2695180002662125 chr3 198022430 97146802 0.4905848393033052 1.2249132410226085 chr4 191154276 78321140 0.4097273764359841 1.8403041742282555 chr5 180915260 84539079 0.46728550703793587 1.1759526567248404 chr6 171115067 85280500 0.4983810104810934 1.4176428871806017 chr7 159138663 77218470 0.4852275904818931 1.6152668815646358 chr8 146364022 70727954 0.48323319510856294 1.3009242442306246 chr9 141213431 65509634 0.463905122452552 2.1978600909960595 chr10 135534747 78259471 0.5774126025409558 4.128583632930058 chr11 135006516 73266096 0.542685628595882 2.1330974468767696 chr12 133851895 67964240 0.5077570250312855 1.3266405526147844 chr13 115169878 40875711 0.3549166822943062 0.9831863025427264 chr14 107349540 47462626 0.4421316197535639 1.172279916811679 chr15 102531392 46275314 0.4513282527169825 1.2000662570913825 chr16 90354753 55967076 0.6194148524759954 3.1972280672382793 chr17 81195210 52347110 0.6447068737182895 1.8227210329427321 chr18 78077248 37290261 0.47760726658808467 2.217779230800317 chr19 59128983 36965936 0.6251745611792444 2.1189018842658265 chr20 63025520 42061418 0.6673712172466011 1.7112386681478042 chr21 48129895 19474107 0.4046156136430383 1.740229447321783 chr22 51304566 25206411 0.49130931153379215 1.3512288509985224 chrMT 16571 3237475 195.3699233600869 156.56189727417842 chrX 155270560 74435291 0.4793908838868102 1.351154623301902 chrY 59373566 3970421 0.06687186348214288 1.9017673971419307