BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714195.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 67,174 number of mapped reads = 40,962 (60.98%) number of supplementary alignments = 1,434 (2.13%) number of secondary alignments = 0 number of mapped bases = 5,218,616 bp number of sequenced bases = 5,131,882 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,008 duplication rate = 39.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.6863 >>>>>>> ACTG content number of A's = 1,401,151 bp (27.3%) number of C's = 1,054,374 bp (20.55%) number of T's = 1,326,056 bp (25.84%) number of G's = 1,350,286 bp (26.31%) number of N's = 15 bp (0%) GC percentage = 46.86% >>>>>>> Mismatches and indels general error rate = 0.0412 number of mismatches = 188,911 number of insertions = 6,499 mapped reads with insertion percentage = 15.27% number of deletions = 15,873 mapped reads with deletion percentage = 36.28% homopolymer indels = 27.52% >>>>>>> Coverage mean coverageData = 0.0017X std coverageData = 0.38X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 510102 0.002046542544020382 0.29896926675365515 chr2 243199373 632455 0.0026005618032576097 1.0621851751057374 chr3 198022430 284901 0.001438730955882119 0.2503932522468244 chr4 191154276 230134 0.0012039176146914966 0.2010698598190725 chr5 180915260 277859 0.0015358516467875623 0.21682900956366383 chr6 171115067 167092 9.764891130247461E-4 0.1430796605227228 chr7 159138663 192042 0.0012067589131372807 0.1732030839826096 chr8 146364022 293428 0.002004782295474225 0.35895580558363704 chr9 141213431 181781 0.0012872784034260877 0.188986201491572 chr10 135534747 241665 0.0017830482983083298 0.22924624848554714 chr11 135006516 205429 0.0015216228526332759 0.19412268926358792 chr12 133851895 198553 0.001483378326470462 0.21161620973984657 chr13 115169878 135784 0.0011789888324792704 0.25136379516405105 chr14 107349540 158814 0.001479410158627601 0.23458186141824222 chr15 102531392 143558 0.00140013704290682 0.2235567106709947 chr16 90354753 227480 0.0025176318062648017 0.35040373396706365 chr17 81195210 194515 0.0023956462456344407 0.2766749528384688 chr18 78077248 109301 0.0013999084598883404 0.1833593216593774 chr19 59128983 136483 0.002308225054369699 0.39211644901627635 chr20 63025520 145458 0.0023079222511769837 0.3155355058375558 chr21 48129895 53817 0.0011181615916677152 0.20568644449666884 chr22 51304566 45709 8.909343468571589E-4 0.13492024084134085 chrMT 16571 23810 1.4368475046768452 13.051348062176757 chrX 155270560 407165 0.002622293627330255 0.27347885508388337 chrY 59373566 21281 3.584254986469905E-4 0.07957651443828723