BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716965.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 = 1,028,961 number of mapped reads = 953,384 (92.66%) number of supplementary alignments = 21,812 (2.12%) number of secondary alignments = 0 number of mapped bases = 74,508,048 bp number of sequenced bases = 74,477,004 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,578 duplication rate = 3.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6218 >>>>>>> ACTG content number of A's = 18,730,268 bp (25.15%) number of C's = 15,006,671 bp (20.15%) number of T's = 22,535,638 bp (30.26%) number of G's = 18,201,366 bp (24.44%) number of N's = 3,061 bp (0%) GC percentage = 44.59% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 504,971 number of insertions = 7,176 mapped reads with insertion percentage = 0.74% number of deletions = 14,934 mapped reads with deletion percentage = 1.54% homopolymer indels = 39.04% >>>>>>> Coverage mean coverageData = 0.0241X std coverageData = 0.2385X There is a 2.09% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8462515 0.033951831157122775 0.4570266382067797 chr2 243199373 7460415 0.03067612760662833 0.25236998730537535 chr3 198022430 4621456 0.02333804306916141 0.16924677099020474 chr4 191154276 3561898 0.01863362972848172 0.2067490731000123 chr5 180915260 4240171 0.023437331930982495 0.17272500968866308 chr6 171115067 4439642 0.025945359913864277 0.18713224710964252 chr7 159138663 4890353 0.03073013752792431 0.282646713304611 chr8 146364022 4452964 0.030423897479395584 0.2538281903059024 chr9 141213431 2214529 0.01568214145296137 0.16470745271028508 chr10 135534747 3932519 0.029014840009993895 0.27739264961611476 chr11 135006516 2243589 0.016618375664179053 0.19121371905029336 chr12 133851895 2537873 0.0189603068376432 0.152864185014815 chr13 115169878 1399618 0.012152639425388643 0.12206109081481643 chr14 107349540 1410910 0.01314313969114353 0.13483359056548727 chr15 102531392 1556164 0.015177439510428182 0.13557240014863414 chr16 90354753 2381237 0.02635430811260145 0.19104782051951238 chr17 81195210 1402503 0.017273223383497623 0.1598188597435891 chr18 78077248 2140348 0.02741321005576426 0.24755888522108377 chr19 59128983 1868983 0.03160857679557925 0.3398871221643141 chr20 63025520 1941966 0.030812375685277962 0.20267586339096533 chr21 48129895 1273701 0.026463822536907676 0.21078149487626782 chr22 51304566 1156389 0.02253968974223464 0.1738311939186391 chrMT 16571 123354 7.4439683784925474 6.109165003027671 chrX 155270560 4506179 0.02902146421060116 0.19813988874996735 chrY 59373566 288772 0.004863645885780214 0.19651508001185858