BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084825.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,667,889 number of mapped reads = 1,537,960 (92.21%) number of supplementary alignments = 11,930 (0.72%) number of secondary alignments = 0 number of mapped bases = 103,842,267 bp number of sequenced bases = 103,802,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,446 duplication rate = 3.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3433 >>>>>>> ACTG content number of A's = 28,797,332 bp (27.74%) number of C's = 18,968,769 bp (18.27%) number of T's = 33,165,453 bp (31.95%) number of G's = 22,855,741 bp (22.02%) number of N's = 15,257 bp (0.01%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 790,420 number of insertions = 8,158 mapped reads with insertion percentage = 0.53% number of deletions = 24,408 mapped reads with deletion percentage = 1.57% homopolymer indels = 49.28% >>>>>>> Coverage mean coverageData = 0.0335X std coverageData = 0.2353X There is a 2.89% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9347022 0.03750049633778044 0.26839423375939536 chr2 243199373 10717902 0.04407043434277275 0.3401493129826449 chr3 198022430 8303538 0.041932310395342585 0.23299741542806204 chr4 191154276 5969729 0.031229900397310495 0.20275076306022333 chr5 180915260 4730708 0.02614875052552228 0.18306181874299593 chr6 171115067 5498789 0.03213503694563612 0.21514666807695038 chr7 159138663 7196889 0.0452240132242408 0.30348201909391376 chr8 146364022 5715229 0.039048045564093616 0.24877585579136083 chr9 141213431 8144491 0.05767504508831033 0.3006765749894916 chr10 135534747 2810273 0.020734705027338856 0.16736644531320585 chr11 135006516 3353453 0.02483919368751061 0.19305776109732786 chr12 133851895 3885071 0.02902514753339876 0.19228625541047978 chr13 115169878 2851434 0.024758504997287573 0.17923699668399687 chr14 107349540 2148553 0.020014552461053863 0.16138891215214773 chr15 102531392 3004464 0.02930286950556567 0.19961742594221793 chr16 90354753 1757032 0.0194459277643092 0.16094851016989747 chr17 81195210 2441870 0.030074064713916007 0.19835270114376147 chr18 78077248 3591681 0.04600163417645048 0.3422292698249756 chr19 59128983 1720759 0.029101785836566814 0.2132231336781176 chr20 63025520 1949530 0.03093239056179148 0.2008801428950047 chr21 48129895 810226 0.016834152661251392 0.15033628456098636 chr22 51304566 729919 0.014227174244101392 0.13339234274520456 chrMT 16571 20714 1.2500150865970672 1.408188071300667 chrX 155270560 6950409 0.044763212034528634 0.2442861155064703 chrY 59373566 192582 0.0032435646529972613 0.07309954260190005