BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237822.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 = 2,518,574 number of mapped reads = 2,309,920 (91.72%) number of supplementary alignments = 21,630 (0.86%) number of secondary alignments = 0 number of mapped bases = 164,062,127 bp number of sequenced bases = 163,978,227 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,323 duplication rate = 8.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.0234 >>>>>>> ACTG content number of A's = 48,158,960 bp (29.37%) number of C's = 31,397,056 bp (19.15%) number of T's = 50,407,240 bp (30.74%) number of G's = 33,717,505 bp (20.56%) number of N's = 297,466 bp (0.18%) GC percentage = 39.71% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,423,857 number of insertions = 12,366 mapped reads with insertion percentage = 0.53% number of deletions = 47,274 mapped reads with deletion percentage = 2.02% homopolymer indels = 46.01% >>>>>>> Coverage mean coverageData = 0.053X std coverageData = 0.7656X There is a 1.66% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.36% of reference with a coverageData >= 5X There is a 0.27% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 9325484 0.037414085319370176 1.4271399211562303 chr2 243199373 13264786 0.05454284621038065 0.6823553140621436 chr3 198022430 5976245 0.030179636720951256 0.42927827711926175 chr4 191154276 15450356 0.08082663031822526 0.7634121260501818 chr5 180915260 15596344 0.08620800699730913 0.7475419961087002 chr6 171115067 11150618 0.06516444282489747 0.6643812278399192 chr7 159138663 10370462 0.0651662003720617 0.8410550485308864 chr8 146364022 6684033 0.04566718588807296 0.8521525187502543 chr9 141213431 6198456 0.043894238360372394 0.6277587474930755 chr10 135534747 4405332 0.03250334026889798 0.5019035454301168 chr11 135006516 3396578 0.0251586227141807 0.42731418638519514 chr12 133851895 5215374 0.03896376663176864 0.49170850020993967 chr13 115169878 5324620 0.04623274846223246 0.5320119683547596 chr14 107349540 4427806 0.041246622947802104 0.5166619983502082 chr15 102531392 6106037 0.05955285382256392 0.6429911958862445 chr16 90354753 8238922 0.09118415718540009 0.8077192698325686 chr17 81195210 3090250 0.03805951114603928 0.5155954914557689 chr18 78077248 4975017 0.0637191643844824 0.9925008178881126 chr19 59128983 2152776 0.03640813507649878 1.1907857935491943 chr20 63025520 2343742 0.037187190204856696 0.48488284930922415 chr21 48129895 3188244 0.06624248816665816 0.69099075649549 chr22 51304566 3064716 0.0597357358017608 0.6503989193981657 chrMT 16571 41057 2.4776416631464606 3.8495016498912404 chrX 155270560 13538831 0.08719509351933812 0.7790145776686009 chrY 59373566 536041 0.009028276994513012 0.23419774332987686