BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617363.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 = 30,315,296 (94.74%) number of supplementary alignments = 66,855 (0.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,226,299 number of mapped paired reads (second in pair) = 15,088,997 number of mapped paired reads (both in pair) = 29,779,640 number of mapped paired reads (singletons) = 535,656 number of mapped bases = 2,975,620,273 bp number of sequenced bases = 2,974,740,997 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,572,369 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 52,668.3962 std insert size = 2,189,544.5173 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 53.4728 >>>>>>> ACTG content number of A's = 899,497,604 bp (30.24%) number of C's = 591,425,160 bp (19.88%) number of T's = 887,363,449 bp (29.83%) number of G's = 594,279,825 bp (19.98%) number of N's = 2,174,959 bp (0.07%) GC percentage = 39.86% >>>>>>> Mismatches and indels general error rate = 0.0114 number of mismatches = 33,161,333 number of insertions = 299,335 mapped reads with insertion percentage = 0.96% number of deletions = 365,470 mapped reads with deletion percentage = 1.17% homopolymer indels = 41.29% >>>>>>> Coverage mean coverageData = 0.9612X std coverageData = 9.8008X There is a 53.16% of reference with a coverageData >= 1X There is a 24.08% of reference with a coverageData >= 2X There is a 9.29% of reference with a coverageData >= 3X There is a 3.27% of reference with a coverageData >= 4X There is a 1.12% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.18% 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 193511757 0.7763742221528909 20.030791750822708 chr2 243199373 293335480 1.2061522872429444 8.83105311332579 chr3 198022430 236536152 1.1944917149032057 1.4520473534479712 chr4 191154276 162697551 0.8511321556835066 9.47883302455826 chr5 180915260 186882302 1.0329825245255706 1.4608156409611908 chr6 171115067 139874485 0.8174293909489572 3.6863296714325644 chr7 159138663 241414850 1.5170094146134683 10.864451666088073 chr8 146364022 125273475 0.8559034746940748 7.474654934227344 chr9 141213431 125275476 0.8871357002861859 14.771282365838294 chr10 135534747 125307117 0.9245386867472443 20.15243731274286 chr11 135006516 159848421 1.1840052297920198 5.583831158175027 chr12 133851895 131413036 0.9817794212028153 1.3565814164721965 chr13 115169878 129638818 1.1256312870280196 1.2933294018800452 chr14 107349540 86080505 0.8018712050373015 1.3734602846202726 chr15 102531392 66886882 0.6523551538244989 0.9778057569582495 chr16 90354753 74698636 0.8267261380261867 7.921676752391436 chr17 81195210 92596124 1.1404136278482437 7.059510644900241 chr18 78077248 53809213 0.6891791703519059 15.326293877808538 chr19 59128983 55272706 0.9347819494882907 9.514525420247372 chr20 63025520 85380383 1.3546954154444104 2.449812634512814 chr21 48129895 47350741 0.983811433621453 3.2472745026996086 chr22 51304566 26548893 0.5174762222917937 0.9208669474134037 chrMT 16571 2052538 123.86325508418321 20.100490422810093 chrX 155270560 123770007 0.797124754364253 3.0436590942497554 chrY 59373566 10164725 0.17119950315936894 8.308244840063912