BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717026.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 = 2,173,383 number of mapped reads = 2,035,811 (93.67%) number of supplementary alignments = 44,394 (2.04%) number of secondary alignments = 0 number of mapped bases = 157,910,097 bp number of sequenced bases = 157,851,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 105,099 duplication rate = 4.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2153 >>>>>>> ACTG content number of A's = 39,912,435 bp (25.28%) number of C's = 33,239,223 bp (21.06%) number of T's = 46,250,261 bp (29.3%) number of G's = 38,443,408 bp (24.35%) number of N's = 6,163 bp (0%) GC percentage = 45.41% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,024,703 number of insertions = 14,285 mapped reads with insertion percentage = 0.69% number of deletions = 28,512 mapped reads with deletion percentage = 1.38% homopolymer indels = 38.7% >>>>>>> Coverage mean coverageData = 0.051X std coverageData = 0.411X There is a 4.1% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17200692 0.06900962545645975 0.7273974311439123 chr2 243199373 14659010 0.060275689937736805 0.43104890191182915 chr3 198022430 10053176 0.0507678650342792 0.27205410123888724 chr4 191154276 9249722 0.04838877891489071 0.38127190522590837 chr5 180915260 9253506 0.05114828898347215 0.27607367934629756 chr6 171115067 9698097 0.056675879979639666 0.29867979070841966 chr7 159138663 14360940 0.09024167810181992 0.7406700893808568 chr8 146364022 9719575 0.06640685919385299 0.4214268260110147 chr9 141213431 4707964 0.03333934999426506 0.28180514860294603 chr10 135534747 8333205 0.061483901246371896 0.5473327732617929 chr11 135006516 4920199 0.03644415948042093 0.31371590442698455 chr12 133851895 5412837 0.04043900162937551 0.2413422608735647 chr13 115169878 2914611 0.02530705988939226 0.18592202675363323 chr14 107349540 2982530 0.02778335147034631 0.20813525893180523 chr15 102531392 3190845 0.03112066400112855 0.2108465500126763 chr16 90354753 4753916 0.05261390067659197 0.29604745480443095 chr17 81195210 2871628 0.03536696314967348 0.2465203939264329 chr18 78077248 4639188 0.05941792415634321 0.4257799010666064 chr19 59128983 3877410 0.06557545561032227 0.5259552011101737 chr20 63025520 4161484 0.06602855478225328 0.3222917915681104 chr21 48129895 2676497 0.05560986576014762 0.3695281393480415 chr22 51304566 2457778 0.047905638652123085 0.2681884914483474 chrMT 16571 30614 1.8474443304568222 1.8590179276984429 chrX 155270560 5337656 0.03437648450549802 0.23571148215994878 chrY 59373566 447017 0.007528889202983024 0.29228213777726647