BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524490.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 = 1,282,838 number of mapped reads = 1,178,727 (91.88%) number of supplementary alignments = 2,736 (0.21%) number of secondary alignments = 0 number of mapped bases = 68,428,384 bp number of sequenced bases = 68,405,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,325 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3886 >>>>>>> ACTG content number of A's = 17,507,508 bp (25.59%) number of C's = 11,450,632 bp (16.74%) number of T's = 22,000,693 bp (32.16%) number of G's = 17,445,698 bp (25.5%) number of N's = 1,423 bp (0%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 318,701 number of insertions = 4,510 mapped reads with insertion percentage = 0.38% number of deletions = 13,043 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.2169X There is a 1.99% of reference with a coverageData >= 1X There is a 0.16% 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 6710156 0.02692132109071054 0.3793973476278837 chr2 243199373 5321333 0.021880537496287048 0.24479406185567631 chr3 198022430 3780353 0.019090529290040528 0.15029590425470996 chr4 191154276 3873073 0.020261503331476614 0.16939166884050783 chr5 180915260 3763440 0.020802225307030485 0.15751346793948737 chr6 171115067 2979133 0.0174101150309575 0.17291190721337202 chr7 159138663 3334113 0.020950992908618318 0.25594262412531027 chr8 146364022 6313161 0.04313328448981813 0.2521760929947244 chr9 141213431 2901262 0.020545227032972523 0.1891612094364359 chr10 135534747 3628025 0.026768227929034317 0.2197080369853985 chr11 135006516 2341955 0.017346977534032505 0.1999345133555868 chr12 133851895 3160534 0.023612172244554325 0.1670250296786186 chr13 115169878 1507795 0.013091921483150307 0.12530335724209618 chr14 107349540 1651987 0.015388859607595897 0.1364687185432653 chr15 102531392 1779661 0.017357230456795124 0.14987977754151532 chr16 90354753 2150522 0.023800872987832747 0.17347534017298458 chr17 81195210 2375482 0.029256430274643048 0.1942694278768593 chr18 78077248 1643766 0.02105307297716231 0.31915028423841296 chr19 59128983 1358994 0.022983551061583455 0.2791528780608233 chr20 63025520 1919833 0.03046120047879018 0.19224920330632406 chr21 48129895 941877 0.019569479634227335 0.1588456258093371 chr22 51304566 539443 0.010514522235701205 0.11066729196411366 chrMT 16571 4955 0.29901635387122083 0.6254983634490618 chrX 155270560 4234720 0.027273167559903177 0.19431357905867716 chrY 59373566 212811 0.0035842718289819412 0.09910591656084314