BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716264.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 = 1,065,908 number of mapped reads = 843,838 (79.17%) number of supplementary alignments = 928 (0.09%) number of secondary alignments = 0 number of mapped bases = 44,473,918 bp number of sequenced bases = 44,462,952 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,884 duplication rate = 6.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9948 >>>>>>> ACTG content number of A's = 8,753,972 bp (19.69%) number of C's = 8,631,680 bp (19.41%) number of T's = 14,863,750 bp (33.43%) number of G's = 12,212,899 bp (27.47%) number of N's = 651 bp (0%) GC percentage = 46.88% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 286,436 number of insertions = 2,429 mapped reads with insertion percentage = 0.29% number of deletions = 6,357 mapped reads with deletion percentage = 0.75% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0144X std coverageData = 0.1538X There is a 1.24% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.03% 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 4383071 0.017584995304786022 0.18026371935940852 chr2 243199373 3921494 0.016124605715985955 0.21945232177545174 chr3 198022430 2922330 0.014757570644901186 0.13869800742908192 chr4 191154276 2844387 0.014880059497073453 0.14553493591908906 chr5 180915260 2651283 0.014654833428644992 0.1380565417030766 chr6 171115067 1930708 0.011283097589530208 0.1360795841551567 chr7 159138663 2551647 0.016034111082107054 0.16257719440254634 chr8 146364022 2744688 0.018752477299373477 0.16345011024553355 chr9 141213431 1973314 0.013973982403982522 0.14522976904340884 chr10 135534747 2278621 0.01681207993106004 0.1700746791652253 chr11 135006516 1916026 0.014192100179816506 0.15049071145312207 chr12 133851895 2146512 0.016036470757474146 0.14536188290594954 chr13 115169878 749862 0.006510921197641626 0.09251078404674001 chr14 107349540 1408773 0.013123232759078427 0.13211575017071925 chr15 102531392 872454 0.008509140303098586 0.10626408440868818 chr16 90354753 1181576 0.01307707631052901 0.14023690641373354 chr17 81195210 1785647 0.021992023913725945 0.17571449412626938 chr18 78077248 1185882 0.015188573244794694 0.15946460334051782 chr19 59128983 1229758 0.02079788857521869 0.19281322180505825 chr20 63025520 1174490 0.01863514969809055 0.1636863733493069 chr21 48129895 604751 0.012564976507844033 0.13599579689992122 chr22 51304566 503513 0.009814194705399126 0.11714490939097601 chrMT 16571 492 0.029690423028181763 0.16973185266351562 chrX 155270560 1380952 0.00889384310844245 0.10985402871633006 chrY 59373566 131687 0.002217939882539647 0.07568528864162267