BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716935.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 577,521 number of mapped reads = 390,937 (67.69%) number of supplementary alignments = 364 (0.06%) number of secondary alignments = 0 number of mapped bases = 20,124,666 bp number of sequenced bases = 20,119,305 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,279 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.866 >>>>>>> ACTG content number of A's = 4,219,658 bp (20.97%) number of C's = 3,424,934 bp (17.02%) number of T's = 6,901,542 bp (34.3%) number of G's = 5,572,805 bp (27.7%) number of N's = 366 bp (0%) GC percentage = 44.72% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 149,078 number of insertions = 1,219 mapped reads with insertion percentage = 0.31% number of deletions = 3,220 mapped reads with deletion percentage = 0.82% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0065X std coverageData = 0.0944X There is a 0.6% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 1956631 0.007850054664457587 0.10344801609596944 chr2 243199373 1717985 0.007064101271346617 0.1343364330276847 chr3 198022430 1326422 0.006698342202951454 0.08806966152425248 chr4 191154276 1220174 0.006383189670316347 0.08786766036055263 chr5 180915260 1232744 0.0068139304556177295 0.08826476074860674 chr6 171115067 886092 0.005178340023091012 0.09186824916450397 chr7 159138663 1179824 0.007413811186788719 0.09977799693511595 chr8 146364022 1257425 0.008591079848844274 0.1007841240607796 chr9 141213431 829415 0.005873485221104783 0.08591301793292892 chr10 135534747 1038710 0.007663791190018601 0.10070978066766584 chr11 135006516 855496 0.00633670155594564 0.08856786557129921 chr12 133851895 970404 0.007249833855546087 0.09144306372491427 chr13 115169878 367335 0.0031895058532579153 0.06124787128304637 chr14 107349540 681034 0.006344079350503039 0.08650127642261893 chr15 102531392 392243 0.003825589337556248 0.06661905240406056 chr16 90354753 539260 0.0059682527160469356 0.08769598525941623 chr17 81195210 819936 0.010098329692108684 0.11015996699622298 chr18 78077248 547098 0.007007137341725979 0.09512517013679275 chr19 59128983 558154 0.009439600880671329 0.11427686784616733 chr20 63025520 515890 0.008185414416255511 0.09963894702435334 chr21 48129895 274528 0.005703897754192067 0.08370920395733371 chr22 51304566 223558 0.004357467910361039 0.07162357400507485 chrMT 16571 15532 0.9373001025888601 1.2037560854297726 chrX 155270560 656280 0.004226686630099099 0.07080113862233223 chrY 59373566 62496 0.0010525896322279176 0.040789820705052195