BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716367.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 = 2,848,352 number of mapped reads = 2,617,159 (91.88%) number of supplementary alignments = 57,547 (2.02%) number of secondary alignments = 0 number of mapped bases = 206,202,371 bp number of sequenced bases = 206,109,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 129,423 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1746 >>>>>>> ACTG content number of A's = 54,173,311 bp (26.28%) number of C's = 41,104,249 bp (19.94%) number of T's = 62,687,904 bp (30.41%) number of G's = 48,128,601 bp (23.35%) number of N's = 15,207 bp (0.01%) GC percentage = 43.29% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,364,250 number of insertions = 18,558 mapped reads with insertion percentage = 0.7% number of deletions = 49,199 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0666X std coverageData = 0.6162X There is a 5.44% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 20619590 0.0827263335083125 1.3978823987297466 chr2 243199373 16846027 0.0692683817075466 0.660556538476398 chr3 198022430 13090423 0.06610575882742172 0.29729967680041786 chr4 191154276 12840392 0.06717292580993585 0.3972615447205278 chr5 180915260 12200744 0.06743899878871468 0.30523134814180486 chr6 171115067 11284599 0.0659474305672919 0.34269528442924246 chr7 159138663 10839718 0.0681149244040086 0.7330564570869518 chr8 146364022 10235105 0.06992910457188721 0.6712393013094329 chr9 141213431 8326745 0.05896567303148381 0.4676748404165916 chr10 135534747 9346173 0.06895776328117542 0.573388299672621 chr11 135006516 11398106 0.08442633983681203 0.6623334497242013 chr12 133851895 8891145 0.06642524560447949 0.3036183655451533 chr13 115169878 7140405 0.061998893495398166 0.29330824980870024 chr14 107349540 6155662 0.05734222987820907 0.31345471749315373 chr15 102531392 6016696 0.05868150117380636 0.28181495202557166 chr16 90354753 4611578 0.05103857679739327 0.29277591570523415 chr17 81195210 6196382 0.076314624963714 0.4160659529033018 chr18 78077248 5363398 0.06869348161451592 0.8357477688583717 chr19 59128983 3770462 0.06376673179039795 0.9036416184313991 chr20 63025520 4159190 0.06599215682790083 0.32044880219915906 chr21 48129895 2685954 0.055806354865307724 0.3305069934938997 chr22 51304566 2201388 0.042908227700435085 0.24156021552944315 chrMT 16571 30027 1.8120210005431174 1.8052478158708993 chrX 155270560 11359094 0.07315677872225101 0.3973250322497749 chrY 59373566 593368 0.00999380768202469 0.32363951733830004