BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818882.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 880,850 number of mapped reads = 869,276 (98.69%) number of supplementary alignments = 13,692 (1.55%) number of secondary alignments = 0 number of mapped bases = 80,478,937 bp number of sequenced bases = 80,427,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,171 duplication rate = 10.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.159 >>>>>>> ACTG content number of A's = 22,195,399 bp (27.6%) number of C's = 17,229,152 bp (21.42%) number of T's = 23,236,724 bp (28.89%) number of G's = 17,764,743 bp (22.09%) number of N's = 1,134 bp (0%) GC percentage = 43.51% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 485,732 number of insertions = 10,252 mapped reads with insertion percentage = 1.14% number of deletions = 25,828 mapped reads with deletion percentage = 2.9% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 0.026X std coverageData = 0.3268X There is a 2.11% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6478111 0.02599035049144371 0.3951036531256337 chr2 243199373 6131209 0.025210628318519553 0.4935238083003063 chr3 198022430 5043830 0.02547100346157756 0.18806887490388052 chr4 191154276 4024453 0.021053429116071668 0.20571652580604272 chr5 180915260 3619931 0.020008986527725744 0.17563036166940582 chr6 171115067 4026399 0.02353035925235035 0.1930366754413224 chr7 159138663 7362169 0.046262604330162056 0.6821212158175554 chr8 146364022 7056992 0.04821534625496968 0.3098796728843378 chr9 141213431 2955793 0.02093138718511839 0.28227691869947896 chr10 135534747 3803612 0.02806374073210909 0.4416315304209329 chr11 135006516 3636736 0.02693748500257573 0.23111674604842353 chr12 133851895 3248910 0.02427242438368168 0.18572961541149344 chr13 115169878 2450249 0.021275085487196574 0.1706539366994777 chr14 107349540 2358073 0.021966307447614585 0.18813616208156672 chr15 102531392 2284465 0.022280639669848626 0.1749151951122751 chr16 90354753 2057139 0.022767357905344503 0.371557126022178 chr17 81195210 2082007 0.02564199292051834 0.22851154592450446 chr18 78077248 1577230 0.020200891301906544 0.33154858565473183 chr19 59128983 1655827 0.02800364416888415 0.35305551222438797 chr20 63025520 3430656 0.054432807535741076 0.29328120707063315 chr21 48129895 795525 0.016528708404620455 0.17159897989956116 chr22 51304566 765175 0.014914364542134515 0.164664559859748 chrMT 16571 37271 2.249170237161306 2.1893040417315617 chrX 155270560 3302104 0.021266774590109033 0.20557957193075063 chrY 59373566 295071 0.004969736869097604 0.40433302346017547