BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818765.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 = 839,637 number of mapped reads = 798,501 (95.1%) number of supplementary alignments = 7,223 (0.86%) number of secondary alignments = 0 number of mapped bases = 54,090,251 bp number of sequenced bases = 54,067,799 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,789 duplication rate = 28.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5869 >>>>>>> ACTG content number of A's = 15,439,021 bp (28.55%) number of C's = 10,783,653 bp (19.94%) number of T's = 15,878,237 bp (29.37%) number of G's = 11,963,605 bp (22.13%) number of N's = 3,283 bp (0.01%) GC percentage = 42.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 276,308 number of insertions = 6,893 mapped reads with insertion percentage = 0.85% number of deletions = 14,160 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.15% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 0.2585X There is a 1.04% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 4484577 0.017992240027357845 0.32685692772916636 chr2 243199373 4864772 0.02000322591292207 0.3727364985541789 chr3 198022430 3675129 0.01855915514217253 0.2132767154599766 chr4 191154276 3260568 0.01705725902778131 0.22294536154795713 chr5 180915260 3418801 0.01889725056913386 0.21764300408503284 chr6 171115067 3084876 0.018028079315774104 0.22852037954330143 chr7 159138663 3005991 0.018889130669647515 0.23089371856663038 chr8 146364022 2857551 0.01952358893225823 0.24224772684843693 chr9 141213431 2342924 0.016591367998133266 0.23014510264492777 chr10 135534747 2595689 0.01915146526964041 0.289510855354671 chr11 135006516 2374879 0.01759084724473595 0.22999503290251055 chr12 133851895 2438238 0.01821593934101568 0.22113909659508005 chr13 115169878 1775641 0.015417581670096065 0.19331804710946282 chr14 107349540 1694918 0.015788777483350183 0.21831649190476146 chr15 102531392 1615920 0.01576024638385871 0.19699161047060548 chr16 90354753 1637216 0.01811986581381059 0.27943511724609543 chr17 81195210 1479892 0.018226346110811215 0.22051512587077726 chr18 78077248 1535128 0.019661656107551332 0.31232415159329596 chr19 59128983 1096827 0.018549735583985944 0.31027304042059806 chr20 63025520 1174154 0.01862981852430571 0.2233614016549475 chr21 48129895 747516 0.015531220253025693 0.20621281022128657 chr22 51304566 674021 0.01313764158924958 0.1926086052354234 chrMT 16571 21757 1.3129563695612818 2.0073714843771717 chrX 155270560 1710143 0.011013955253333279 0.1740473753894354 chrY 59373566 523123 0.008810705424026578 0.4335734655800878