BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716728.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 = 1,412,845 number of mapped reads = 1,304,696 (92.35%) number of supplementary alignments = 32,409 (2.29%) number of secondary alignments = 0 number of mapped bases = 100,337,880 bp number of sequenced bases = 100,301,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,132 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8359 >>>>>>> ACTG content number of A's = 25,966,818 bp (25.89%) number of C's = 19,704,962 bp (19.65%) number of T's = 30,141,329 bp (30.05%) number of G's = 24,476,062 bp (24.4%) number of N's = 12,258 bp (0.01%) GC percentage = 44.05% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 734,639 number of insertions = 8,017 mapped reads with insertion percentage = 0.61% number of deletions = 21,415 mapped reads with deletion percentage = 1.62% homopolymer indels = 39.79% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.2927X There is a 2.89% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% 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 10326902 0.04143180048486218 0.45528671971536877 chr2 243199373 8097513 0.033295780742000514 0.4156033927629955 chr3 198022430 8154209 0.041178208953399874 0.2258395589841244 chr4 191154276 4077518 0.02133103211355837 0.1670783763022754 chr5 180915260 6434135 0.035564357589293466 0.20781676166420326 chr6 171115067 6699180 0.03915014684241686 0.24950834256709778 chr7 159138663 4774711 0.03000346308049603 0.41253497483853996 chr8 146364022 6898848 0.04713486214528868 0.3665423444295342 chr9 141213431 5281328 0.037399615338288894 0.27106847122022154 chr10 135534747 5507914 0.040638390685157656 0.28712796181352535 chr11 135006516 4503800 0.03335987131169284 0.2449933634296007 chr12 133851895 3446214 0.025746471501206614 0.1754369406991118 chr13 115169878 3013321 0.0261641416343256 0.17461247344600397 chr14 107349540 2034936 0.018956168792153186 0.16936611597296267 chr15 102531392 2010549 0.019609106643163492 0.15032193313167133 chr16 90354753 2439119 0.026994916360404415 0.19311972644808897 chr17 81195210 2893361 0.03563462672243843 0.2284106663129334 chr18 78077248 2915519 0.03734146726073132 0.4843695193191204 chr19 59128983 1681430 0.02843664671181644 0.35373343417330855 chr20 63025520 1897020 0.03009923599202355 0.20873771356670479 chr21 48129895 2082337 0.043264939597312646 0.23547802877140905 chr22 51304566 1371201 0.026726685496179813 0.17940500338967658 chrMT 16571 98178 5.92468770744071 4.455180177821085 chrX 155270560 3492453 0.022492692755149462 0.19651455016713582 chrY 59373566 206184 0.0034726565017166055 0.10856923097171957