BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716578.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 = 1,877,551 number of mapped reads = 1,709,669 (91.06%) number of supplementary alignments = 10,397 (0.55%) number of secondary alignments = 0 number of mapped bases = 100,000,557 bp number of sequenced bases = 99,971,983 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,798 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4881 >>>>>>> ACTG content number of A's = 25,991,290 bp (26%) number of C's = 19,395,250 bp (19.4%) number of T's = 31,328,483 bp (31.34%) number of G's = 23,255,671 bp (23.26%) number of N's = 1,289 bp (0%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 498,490 number of insertions = 6,289 mapped reads with insertion percentage = 0.37% number of deletions = 17,988 mapped reads with deletion percentage = 1.04% homopolymer indels = 40.86% >>>>>>> Coverage mean coverageData = 0.0323X std coverageData = 0.3166X There is a 2.88% of reference with a coverageData >= 1X There is a 0.24% 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 0.01% 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 7132910 0.028617421177859374 0.4042158135901955 chr2 243199373 9880371 0.040626630233952125 0.37859985619539843 chr3 198022430 7697499 0.038871854062188814 0.22915984223901634 chr4 191154276 5629650 0.02945081908604545 0.20392498176186669 chr5 180915260 5095598 0.02816566164733699 0.1837235538052966 chr6 171115067 5595524 0.03270035829165178 0.21299711109962685 chr7 159138663 6442291 0.04048224911880779 0.7519042635190216 chr8 146364022 7267587 0.049654190290015394 0.33384248454661364 chr9 141213431 4261767 0.030179615138732803 0.22708638943374504 chr10 135534747 4775932 0.03523769443418078 0.41650939063280973 chr11 135006516 2991092 0.022155167680943638 0.2091556108100889 chr12 133851895 4710380 0.03519098478209815 0.23045910257590754 chr13 115169878 2651991 0.02302677615061813 0.16516478406476545 chr14 107349540 3277574 0.030531793615510602 0.19556391965434045 chr15 102531392 2424324 0.023644699956867844 0.16987040250704746 chr16 90354753 3055960 0.0338217957388473 0.21251810502039487 chr17 81195210 4166446 0.05131393834685568 0.2588418044301402 chr18 78077248 2372846 0.030391004559996788 0.3641068332264798 chr19 59128983 2040019 0.03450116840331923 0.37600137397780664 chr20 63025520 2300969 0.036508528608728656 0.2205293176769601 chr21 48129895 822230 0.01708356105908812 0.15261445808312818 chr22 51304566 1546975 0.03015277431642244 0.1889478820414275 chrMT 16571 140829 8.498521513487418 5.575907144444666 chrX 155270560 3502781 0.022559208906054052 0.18625500553975835 chrY 59373566 217012 0.003655027222046929 0.09647068643301912