BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524860.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 = 1,374,811 number of mapped reads = 1,260,976 (91.72%) number of supplementary alignments = 6,561 (0.48%) number of secondary alignments = 0 number of mapped bases = 73,350,022 bp number of sequenced bases = 73,328,719 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,967 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7377 >>>>>>> ACTG content number of A's = 18,504,918 bp (25.24%) number of C's = 12,870,279 bp (17.55%) number of T's = 23,109,509 bp (31.51%) number of G's = 18,834,321 bp (25.68%) number of N's = 9,692 bp (0.01%) GC percentage = 43.24% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 352,476 number of insertions = 5,012 mapped reads with insertion percentage = 0.4% number of deletions = 13,480 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.76% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2454X There is a 2.19% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.01% 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 6135201 0.0246145866172185 0.4744940033177107 chr2 243199373 4755726 0.019554844822729046 0.2589779613556066 chr3 198022430 5225836 0.02639012156350167 0.17158571232605768 chr4 191154276 3956262 0.02069669631664426 0.1631732054727111 chr5 180915260 4436744 0.024523879301281717 0.16587458691551732 chr6 171115067 4785226 0.02796495997631816 0.19465305198166036 chr7 159138663 3335960 0.020962599139091674 0.3259536439942998 chr8 146364022 7859604 0.05369901627874096 0.3213966142552526 chr9 141213431 3024421 0.021417374952103527 0.19922390063073456 chr10 135534747 3652425 0.026948255564309277 0.23443694596078046 chr11 135006516 3522693 0.026092762811537187 0.21043586219866176 chr12 133851895 2891057 0.021598924692100924 0.15787536665734067 chr13 115169878 1908403 0.016570331002694994 0.13548583913476014 chr14 107349540 1517664 0.014137592019490722 0.13350170812274265 chr15 102531392 2159862 0.02106537283722823 0.15369810203801249 chr16 90354753 2149468 0.02378920785716718 0.17336781689090958 chr17 81195210 2075759 0.025565042568397815 0.18282638157374817 chr18 78077248 1774038 0.022721574407950446 0.3584207111246534 chr19 59128983 1157043 0.019568119411084748 0.3130298643076462 chr20 63025520 1621924 0.0257344009220392 0.17118372633058024 chr21 48129895 1058144 0.021985171586183596 0.16440937497977 chr22 51304566 475240 0.009263113150591704 0.10079846558440542 chrMT 16571 21937 1.323818719449641 1.4161458287994315 chrX 155270560 3662808 0.0235898421439325 0.18292377162350368 chrY 59373566 186577 0.003142425368218577 0.08422960575676815