BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716792.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 = 1,613,702 number of mapped reads = 1,412,524 (87.53%) number of supplementary alignments = 4,640 (0.29%) number of secondary alignments = 0 number of mapped bases = 79,910,499 bp number of sequenced bases = 79,886,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,604 duplication rate = 1.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2967 >>>>>>> ACTG content number of A's = 20,036,510 bp (25.08%) number of C's = 15,296,930 bp (19.15%) number of T's = 25,473,436 bp (31.89%) number of G's = 19,079,373 bp (23.88%) number of N's = 499 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 414,827 number of insertions = 5,840 mapped reads with insertion percentage = 0.41% number of deletions = 14,992 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.2245X There is a 2.35% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 6709175 0.026917385293094214 0.25763445587848743 chr2 243199373 6327267 0.02601678993637866 0.35150771456884705 chr3 198022430 4648911 0.023476688979122213 0.1672402894677369 chr4 191154276 4925624 0.02576779396763272 0.18527729781567046 chr5 180915260 4613744 0.025502237898560907 0.1714999439176251 chr6 171115067 4307137 0.025170997946078005 0.20367791594995477 chr7 159138663 4593700 0.028866021074966552 0.31258473860135305 chr8 146364022 4189073 0.028620920242271013 0.2147836800728166 chr9 141213431 2663539 0.018861796509993443 0.16878384976447774 chr10 135534747 3525856 0.02601440647541106 0.266918372058942 chr11 135006516 2847922 0.021094700347648404 0.19117905937145332 chr12 133851895 4014873 0.029994890995006084 0.18747316697325472 chr13 115169878 2454351 0.021310702439052684 0.1572846166157029 chr14 107349540 2702234 0.02517229230791301 0.17873677620624942 chr15 102531392 2943256 0.028705901115631007 0.18888345083470948 chr16 90354753 2762826 0.030577539180478973 0.19930951753954357 chr17 81195210 3542686 0.04363171177215996 0.2371633689072506 chr18 78077248 1479088 0.018943905399944425 0.26028635651085713 chr19 59128983 1955349 0.03306921412803599 0.25823181221993785 chr20 63025520 2280109 0.036177551569586415 0.21367327127691801 chr21 48129895 985621 0.020478353422545385 0.1652494824563997 chr22 51304566 730351 0.014235594547276747 0.129412044701376 chrMT 16571 45734 2.7598817210789934 2.5661322320749513 chrX 155270560 4419426 0.02846274271181865 0.1931524385506618 chrY 59373566 242647 0.004086785018100479 0.11222288260578606