BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6003990.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 = 2,329,390 number of mapped reads = 1,679,619 (72.11%) number of supplementary alignments = 10,416 (0.45%) number of secondary alignments = 0 number of mapped bases = 107,597,335 bp number of sequenced bases = 107,540,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 267,978 duplication rate = 12.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1498 >>>>>>> ACTG content number of A's = 29,092,376 bp (27.05%) number of C's = 18,585,928 bp (17.28%) number of T's = 36,301,917 bp (33.76%) number of G's = 23,549,924 bp (21.9%) number of N's = 10,527 bp (0.01%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 1,112,597 number of insertions = 9,438 mapped reads with insertion percentage = 0.56% number of deletions = 34,286 mapped reads with deletion percentage = 2.02% homopolymer indels = 49.52% >>>>>>> Coverage mean coverageData = 0.0348X std coverageData = 0.3966X There is a 1.82% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 10954078 0.04394804697397323 0.6046741434436638 chr2 243199373 10484604 0.04311114733013724 0.5112248758380225 chr3 198022430 7367912 0.0372074618011707 0.3303853914280192 chr4 191154276 6733184 0.03522382099367738 0.3249470274525934 chr5 180915260 6079789 0.03360572789713814 0.31261069280716786 chr6 171115067 7213628 0.042156591622641855 0.384459738231735 chr7 159138663 5468407 0.03436252948788441 0.4080615948635172 chr8 146364022 6995319 0.04779397904219932 0.5246879061665543 chr9 141213431 3868760 0.027396544171495982 0.36325405921310633 chr10 135534747 4478707 0.033044714356533236 0.3544883192576986 chr11 135006516 4247565 0.0314619258821552 0.36720664594581304 chr12 133851895 4273199 0.03192483005190177 0.30517988645102473 chr13 115169878 2391690 0.020766627885114197 0.24447685176786718 chr14 107349540 2517400 0.023450496387781447 0.27469647385022267 chr15 102531392 2603649 0.025393676504460214 0.27136791926862197 chr16 90354753 3392359 0.03754488709631025 0.33251902637429925 chr17 81195210 2400061 0.029559145176174802 0.294127516448293 chr18 78077248 3186722 0.04081498876599749 0.622642367624069 chr19 59128983 1788618 0.030249429454925682 0.4123641237732395 chr20 63025520 2432426 0.038594302752281935 0.33519474842349656 chr21 48129895 1961286 0.04074984996331282 0.3527196207417888 chr22 51304566 1193220 0.023257579062261242 0.24614628564094965 chrMT 16571 83546 5.0416993542936455 5.335721469157884 chrX 155270560 5225158 0.033651955657273344 0.3258980376812867 chrY 59373566 256048 0.004312491521900504 0.11085736531160575