BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716862.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 = 917,313 number of mapped reads = 872,454 (95.11%) number of supplementary alignments = 18,816 (2.05%) number of secondary alignments = 0 number of mapped bases = 68,353,348 bp number of sequenced bases = 68,326,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,836 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8213 >>>>>>> ACTG content number of A's = 17,406,285 bp (25.48%) number of C's = 14,810,695 bp (21.68%) number of T's = 19,663,247 bp (28.78%) number of G's = 16,444,052 bp (24.07%) number of N's = 2,586 bp (0%) GC percentage = 45.74% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 420,169 number of insertions = 5,348 mapped reads with insertion percentage = 0.6% number of deletions = 12,858 mapped reads with deletion percentage = 1.45% homopolymer indels = 40.54% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2135X There is a 1.97% of reference with a coverageData >= 1X There is a 0.17% 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 7491870 0.03005757807118964 0.3845506830866314 chr2 243199373 6400768 0.02631901522213217 0.22554693645062307 chr3 198022430 4361306 0.022024303004462675 0.16370435028666597 chr4 191154276 3255738 0.017031991478966446 0.18260629039930124 chr5 180915260 4059140 0.022436692183953968 0.16506316633114887 chr6 171115067 3851051 0.022505621904119057 0.16975637612373867 chr7 159138663 4235879 0.026617535425693502 0.2655516244030856 chr8 146364022 4239360 0.028964495113423434 0.22669122634498104 chr9 141213431 2044050 0.014474897929503603 0.14998755284274742 chr10 135534747 3656757 0.026980217847752355 0.289098866672884 chr11 135006516 2901808 0.02149383663822567 0.1843816759429028 chr12 133851895 2574503 0.019233967513123368 0.1515294043794532 chr13 115169878 1262698 0.01096378690268301 0.11256423246144619 chr14 107349540 1316647 0.012265045569827314 0.12677379090658142 chr15 102531392 1421527 0.013864309966649044 0.1271124552581914 chr16 90354753 2058246 0.02277960961278927 0.1706336875799729 chr17 81195210 1248369 0.01537490943123369 0.1488224453746153 chr18 78077248 2005826 0.025690275353967396 0.21433291631974882 chr19 59128983 1688472 0.02855574228293424 0.28037749367509607 chr20 63025520 1871249 0.02969033813604394 0.19441178828039213 chr21 48129895 744196 0.015462240256289776 0.16454698954999492 chr22 51304566 1084347 0.02113548723908901 0.16182744742130736 chrMT 16571 16177 0.9762235230221471 1.2988306589726735 chrX 155270560 4334234 0.02791407463204873 0.1869698895668666 chrY 59373566 229130 0.0038591247829042304 0.1500700860584779