BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 962,362 number of mapped reads = 811,537 (84.33%) number of supplementary alignments = 4,368 (0.45%) number of secondary alignments = 0 number of mapped bases = 53,755,287 bp number of sequenced bases = 53,727,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,513 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6006 >>>>>>> ACTG content number of A's = 14,996,126 bp (27.91%) number of C's = 9,476,353 bp (17.64%) number of T's = 17,311,034 bp (32.22%) number of G's = 11,924,032 bp (22.19%) number of N's = 20,219 bp (0.04%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 453,052 number of insertions = 4,155 mapped reads with insertion percentage = 0.51% number of deletions = 15,943 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.4% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 0.2072X There is a 1.6% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5280141 0.021184063569494576 0.30923745718792345 chr2 243199373 4858313 0.019976667456293153 0.22541792321594095 chr3 198022430 3566199 0.01800906594268134 0.14159849696520643 chr4 191154276 2724614 0.014253481831607052 0.13395484698728644 chr5 180915260 3121502 0.01725394530013665 0.13979600465094338 chr6 171115067 4972698 0.029060550231967592 0.23072990088855294 chr7 159138663 2977457 0.01870982791906452 0.2439032833392936 chr8 146364022 3256898 0.02225203950735926 0.43547558376618845 chr9 141213431 2295608 0.01625630071972403 0.18762255870380218 chr10 135534747 1922723 0.01418619979421218 0.1618478188299627 chr11 135006516 2208994 0.01636212877310307 0.1783446553333975 chr12 133851895 2174053 0.01624222802374221 0.13691899076403086 chr13 115169878 1912382 0.016604879966964973 0.13612163143841655 chr14 107349540 1639967 0.01527688893683196 0.13799638119671784 chr15 102531392 1201233 0.011715758233341844 0.11855620010480306 chr16 90354753 1242608 0.013752547140491879 0.1352473028338402 chr17 81195210 975673 0.012016386188298546 0.12485369995929624 chr18 78077248 1654387 0.02118910492337025 0.2999892586233686 chr19 59128983 886969 0.015000579326723749 0.20112327594983703 chr20 63025520 1065608 0.016907563793206307 0.14128326998783777 chr21 48129895 955901 0.019860857789114228 0.1569474553880022 chr22 51304566 687233 0.013395162528029182 0.12184389819879882 chrMT 16571 30849 1.8616257316999578 1.6987969249887347 chrX 155270560 2019293 0.01300499592453328 0.12830478832792971 chrY 59373566 123984 0.0020882020123231273 0.07033356614464616