BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525126.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 = 1,384,910 number of mapped reads = 1,278,549 (92.32%) number of supplementary alignments = 5,780 (0.42%) number of secondary alignments = 0 number of mapped bases = 74,902,398 bp number of sequenced bases = 74,882,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,921 duplication rate = 1.96% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0937 >>>>>>> ACTG content number of A's = 20,126,895 bp (26.88%) number of C's = 14,467,902 bp (19.32%) number of T's = 23,481,661 bp (31.36%) number of G's = 16,803,953 bp (22.44%) number of N's = 2,181 bp (0%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 351,826 number of insertions = 4,929 mapped reads with insertion percentage = 0.38% number of deletions = 12,061 mapped reads with deletion percentage = 0.94% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.0242X std coverageData = 0.2261X There is a 2.2% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 6236470 0.02502088048960167 0.42585993866133937 chr2 243199373 6252405 0.0257089684190921 0.21063175790659508 chr3 198022430 4723802 0.023854883509913497 0.16539529095207073 chr4 191154276 5229954 0.027359858798031805 0.18835742680262169 chr5 180915260 4802330 0.026544637528089117 0.17545007329759074 chr6 171115067 4665440 0.027264928108288677 0.19036291290290544 chr7 159138663 2884885 0.018128121385561722 0.18343173093709506 chr8 146364022 3946180 0.026961407223422707 0.2763695216954671 chr9 141213431 3288025 0.023284081242952025 0.200763195090068 chr10 135534747 3178078 0.023448437174564542 0.20622732427557308 chr11 135006516 3218968 0.023843056582543022 0.20024180591604718 chr12 133851895 3578427 0.02673422740858469 0.178819355598461 chr13 115169878 2454585 0.0213127342203141 0.15672944314727585 chr14 107349540 2411731 0.022466151228966606 0.1673871144053826 chr15 102531392 2099850 0.020480069167499452 0.15431147942880175 chr16 90354753 2230706 0.024688308317327812 0.17622659266595958 chr17 81195210 2019855 0.024876529046479467 0.1775249865459875 chr18 78077248 2224372 0.028489375035349606 0.36559043979120864 chr19 59128983 1426397 0.024123482725890957 0.31262905194804824 chr20 63025520 1406760 0.02232048224274865 0.16548558587354295 chr21 48129895 1026082 0.02131901596710319 0.16614615631296012 chr22 51304566 857237 0.01670878572484172 0.1384556989276147 chrMT 16571 25267 1.5247721923842859 1.5103543942596085 chrX 155270560 4504757 0.029012306003147022 0.19916605022878328 chrY 59373566 209835 0.003534148513161564 0.08943863924029932