BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716970.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 = 2,415,870 number of mapped reads = 2,110,716 (87.37%) number of supplementary alignments = 7,049 (0.29%) number of secondary alignments = 0 number of mapped bases = 119,579,482 bp number of sequenced bases = 119,544,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,574 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9285 >>>>>>> ACTG content number of A's = 30,362,833 bp (25.4%) number of C's = 23,521,100 bp (19.68%) number of T's = 37,444,498 bp (31.32%) number of G's = 28,214,189 bp (23.6%) number of N's = 1,786 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 609,127 number of insertions = 8,333 mapped reads with insertion percentage = 0.39% number of deletions = 22,459 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.89% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3609X There is a 3.39% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9768675 0.03919217918417944 0.4281038613230517 chr2 243199373 11646946 0.04789052642828976 0.4850332057493671 chr3 198022430 9844847 0.04971581754652743 0.27024578534907767 chr4 191154276 6736486 0.035241094999099054 0.21696332065527074 chr5 180915260 6391269 0.03532741793036143 0.20903462894894428 chr6 171115067 6664657 0.03894839371450557 0.25676384047376516 chr7 159138663 7428746 0.04668096275259017 0.8863304130042886 chr8 146364022 8309089 0.05677002371525428 0.3352318528073046 chr9 141213431 4897792 0.03468361306227309 0.24869990837232364 chr10 135534747 5596453 0.04129164752120724 0.463764889817203 chr11 135006516 4022478 0.02979469524270962 0.2448665597333879 chr12 133851895 5609121 0.04190542838411066 0.24483551556548425 chr13 115169878 3113367 0.027032823634666 0.18315863487129735 chr14 107349540 2993794 0.027888279726210285 0.19335793194158532 chr15 102531392 2820021 0.027503976538229384 0.18800316303067166 chr16 90354753 3570132 0.039512387356091826 0.23823073800363162 chr17 81195210 4895424 0.060292029542136784 0.2909101573851152 chr18 78077248 2779728 0.03560227942460267 0.3987315549760128 chr19 59128983 2403791 0.040653345923436564 0.4108359678687375 chr20 63025520 2600492 0.041260936839553244 0.2360338259295536 chr21 48129895 1221031 0.02536949228748577 0.1845411100719433 chr22 51304566 1681496 0.03277478265774629 0.20326541101802373 chrMT 16571 66711 4.025767907790719 3.208405650737378 chrX 155270560 4257409 0.027419293135801145 0.22273507555009547 chrY 59373566 259527 0.0043710866212751985 0.10545664206881626