BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8751177.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP188831/SRP188831.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 = 5,550,290 number of mapped reads = 4,416,507 (79.57%) number of supplementary alignments = 251,581 (4.53%) number of secondary alignments = 0 number of mapped bases = 432,421,041 bp number of sequenced bases = 432,266,654 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 173,569 duplication rate = 1.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.8695 >>>>>>> ACTG content number of A's = 128,693,459 bp (29.77%) number of C's = 87,452,831 bp (20.23%) number of T's = 129,361,535 bp (29.93%) number of G's = 86,755,720 bp (20.07%) number of N's = 3,109 bp (0%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,757,480 number of insertions = 278,400 mapped reads with insertion percentage = 6.06% number of deletions = 68,700 mapped reads with deletion percentage = 1.52% homopolymer indels = 52.19% >>>>>>> Coverage mean coverageData = 0.1397X std coverageData = 1.7823X There is a 10.89% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 40141449 0.1610485415801632 5.170471536640863 chr2 243199373 33776075 0.13888224539131522 0.7172892830769784 chr3 198022430 28417022 0.14350405658591303 0.5979538133579057 chr4 191154276 25220344 0.13193711659371932 0.566582392943979 chr5 180915260 44211951 0.24437933538608075 0.6062785341743161 chr6 171115067 22347366 0.13059847032640323 0.7653192093132333 chr7 159138663 25573601 0.1607001122034059 0.9899200867232558 chr8 146364022 21623427 0.147737310744303 1.1375703718429777 chr9 141213431 19178620 0.13581300209326405 0.9040612860967517 chr10 135534747 18963309 0.13991474083026104 2.474385365401399 chr11 135006516 18947632 0.1403460555933463 0.6864532182964626 chr12 133851895 19174329 0.14325033650065247 0.45894619115888546 chr13 115169878 17460650 0.15160778411174491 0.46084143603737227 chr14 107349540 11113862 0.10352966580015155 0.41738861797305343 chr15 102531392 10007541 0.09760465360696556 0.36376497592380636 chr16 90354753 11762304 0.1301791395522934 0.9724612729785143 chr17 81195210 11415143 0.14058887217608035 0.7098327025619082 chr18 78077248 7681512 0.09838348810654801 1.9680991571697297 chr19 59128983 7793202 0.13180003451099437 3.515599457552704 chr20 63025520 7670073 0.12169789317089331 0.4388941868326674 chr21 48129895 4821697 0.1001809166631259 0.4621600223371251 chr22 51304566 2808763 0.05474684261046083 0.27545776607031636 chrMT 16571 236994 14.301731941343311 8.165496695352065 chrX 155270560 20606523 0.13271365157696347 0.5033173209757488 chrY 59373566 1467652 0.024718946475271505 1.1092673020853614