BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716277.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 = 32,419,461 number of mapped reads = 31,644,682 (97.61%) number of supplementary alignments = 18,078 (0.06%) number of secondary alignments = 0 number of mapped bases = 2,142,478,231 bp number of sequenced bases = 2,142,106,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,720,831 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7768 >>>>>>> ACTG content number of A's = 595,518,737 bp (27.8%) number of C's = 467,796,119 bp (21.84%) number of T's = 621,014,070 bp (28.99%) number of G's = 457,418,833 bp (21.35%) number of N's = 358,528 bp (0.02%) GC percentage = 43.19% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 7,625,950 number of insertions = 182,351 mapped reads with insertion percentage = 0.57% number of deletions = 187,509 mapped reads with deletion percentage = 0.59% homopolymer indels = 36.72% >>>>>>> Coverage mean coverageData = 0.6921X std coverageData = 7.1777X There is a 44.56% of reference with a coverageData >= 1X There is a 15.28% of reference with a coverageData >= 2X There is a 4.43% of reference with a coverageData >= 3X There is a 1.23% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211065425 0.8467999965384239 14.05369763580764 chr2 243199373 183185572 0.7532320899527977 5.719759807709408 chr3 198022430 133861753 0.6759928812104771 3.779698583294834 chr4 191154276 105413240 0.5514563535057934 4.96112693280761 chr5 180915260 125095059 0.6914566466090257 1.0844372660412553 chr6 171115067 128287071 0.7497123032421219 2.270638322896715 chr7 159138663 122486697 0.7696853466715377 5.08869315757377 chr8 146364022 161547659 1.1037388614532606 4.14132753610242 chr9 141213431 80910026 0.5729626808656749 2.9749113790208277 chr10 135534747 111005317 0.8190174066580874 22.055060070743224 chr11 135006516 110378147 0.8175764420141025 2.661900124050713 chr12 133851895 73523392 0.5492891378190798 1.1968883243049178 chr13 115169878 52348472 0.45453266868963776 0.7679550315311754 chr14 107349540 44711999 0.4165085290537808 1.2867608341129826 chr15 102531392 56907529 0.555025420897436 0.8747630089493226 chr16 90354753 72574279 0.803214845820009 5.448702757706936 chr17 81195210 55905663 0.688534003422123 2.0921880291465387 chr18 78077248 54533490 0.6984555859345862 6.328945114943701 chr19 59128983 47449606 0.8024762746215337 9.931016409675651 chr20 63025520 44080222 0.6994027498702113 1.926979088643786 chr21 48129895 22473552 0.4669354047001349 4.658719878866803 chr22 51304566 42377682 0.8260021534925371 1.411000981817665 chrMT 16571 4894745 295.38018224609255 80.51679918427189 chrX 155270560 89007153 0.5732390802222906 1.7768309786336218 chrY 59373566 8454481 0.14239469800415896 6.980102752584139