BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238535.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 = 2,680,376 number of mapped reads = 2,352,213 (87.76%) number of supplementary alignments = 21,414 (0.8%) number of secondary alignments = 0 number of mapped bases = 144,172,559 bp number of sequenced bases = 144,082,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 860,331 duplication rate = 22.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0037 >>>>>>> ACTG content number of A's = 35,026,341 bp (24.31%) number of C's = 25,456,207 bp (17.67%) number of T's = 48,498,998 bp (33.66%) number of G's = 35,092,136 bp (24.36%) number of N's = 9,276 bp (0.01%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 930,167 number of insertions = 9,443 mapped reads with insertion percentage = 0.4% number of deletions = 52,763 mapped reads with deletion percentage = 2.22% homopolymer indels = 40.29% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.9016X There is a 1.6% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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% 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 21060216 0.0844941365261433 1.1396195579749204 chr2 243199373 13463931 0.055361701117543585 2.1958570303604867 chr3 198022430 15219552 0.0768577175828011 0.6876923158992196 chr4 191154276 1662633 0.008697859314431448 0.18518844486706162 chr5 180915260 4669807 0.02581212331121211 0.39273102868588305 chr6 171115067 1410401 0.008242412691805801 0.5967408694169913 chr7 159138663 10629921 0.06679659612321866 0.7745602941233329 chr8 146364022 9124945 0.062344180457134475 0.685191597208854 chr9 141213431 2702201 0.01913558066583624 0.3960102205242329 chr10 135534747 13394654 0.09882819200599534 0.8302911843790022 chr11 135006516 6910990 0.051190047745547335 0.5733056009504433 chr12 133851895 1187626 0.00887268723390132 0.21789419387034048 chr13 115169878 7554592 0.06559520710788631 0.7393019323040977 chr14 107349540 2026397 0.018876624902165393 0.3426276766287422 chr15 102531392 661005 0.006446854832518025 0.4401579722323075 chr16 90354753 7092072 0.07849141040759637 0.74801951729235 chr17 81195210 3007236 0.03703711093302179 0.4708998616145152 chr18 78077248 3727453 0.04774057866383815 1.6128623089789298 chr19 59128983 4392190 0.07428150759839722 0.8381909824956032 chr20 63025520 3930285 0.06236021535403437 0.6379430451049234 chr21 48129895 752295 0.015630514049532 0.2964727412129428 chr22 51304566 263763 0.005141121357502566 0.1266022259829798 chrMT 16571 37728 2.2767485366000844 3.5626577585682195 chrX 155270560 8839250 0.0569280486912651 0.5838900421885169 chrY 59373566 451416 0.007602979413431223 0.3045350922435267