BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524687.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 = 1,940,036 number of mapped reads = 1,791,290 (92.33%) number of supplementary alignments = 7,549 (0.39%) number of secondary alignments = 0 number of mapped bases = 106,689,810 bp number of sequenced bases = 106,656,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,471 duplication rate = 2.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9931 >>>>>>> ACTG content number of A's = 28,244,395 bp (26.48%) number of C's = 19,150,509 bp (17.96%) number of T's = 33,150,022 bp (31.08%) number of G's = 26,095,695 bp (24.47%) number of N's = 15,625 bp (0.01%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 535,843 number of insertions = 7,562 mapped reads with insertion percentage = 0.42% number of deletions = 20,997 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.3272X There is a 3.07% of reference with a coverageData >= 1X There is a 0.27% 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 8550968 0.0343067069028486 0.6166914686581069 chr2 243199373 9038685 0.03716574137713751 0.4242368850277938 chr3 198022430 7133238 0.03602237382906573 0.20935507045705218 chr4 191154276 7011330 0.03667890746006645 0.2511199036342862 chr5 180915260 6449335 0.03564837482476602 0.20856357048904944 chr6 171115067 6141432 0.035890655964269935 0.2355236444756982 chr7 159138663 5890510 0.037014952174130054 0.3510663757225813 chr8 146364022 5411877 0.03697545972055892 0.3892544029965992 chr9 141213431 4488906 0.03178809528393939 0.26649436748048483 chr10 135534747 5210474 0.038443824298428804 0.35325914386355245 chr11 135006516 4891421 0.03623099939857718 0.27237387235842075 chr12 133851895 4786553 0.03576006899267283 0.21054521539131205 chr13 115169878 3363755 0.029206899046988657 0.18713298177952542 chr14 107349540 3174895 0.02957530139393238 0.19701349384349776 chr15 102531392 3029296 0.029545058746495902 0.18879882014976382 chr16 90354753 3089321 0.03419101815263664 0.22661420437065888 chr17 81195210 2827891 0.03482829836883235 0.21778536104305454 chr18 78077248 2830317 0.0362502146592052 0.4943435346639874 chr19 59128983 2160702 0.036542181014681076 0.45523376396691906 chr20 63025520 2245526 0.035628837334463884 0.21284204499920603 chr21 48129895 1412705 0.029351923580967713 0.22250368626094894 chr22 51304566 1246010 0.024286532313712583 0.17122095476769136 chrMT 16571 11480 0.6927765373242412 0.9841944117244015 chrX 155270560 5927813 0.03817731448897975 0.2342758496300169 chrY 59373566 365370 0.0061537486227456846 0.22563165080846478