BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237332.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 = 3,310,853 number of mapped reads = 2,549,604 (77.01%) number of supplementary alignments = 29,279 (0.88%) number of secondary alignments = 0 number of mapped bases = 151,040,662 bp number of sequenced bases = 150,934,660 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 795,790 duplication rate = 22.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9213 >>>>>>> ACTG content number of A's = 38,986,734 bp (25.83%) number of C's = 26,304,493 bp (17.43%) number of T's = 50,359,487 bp (33.37%) number of G's = 35,268,778 bp (23.37%) number of N's = 15,168 bp (0.01%) GC percentage = 40.79% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,103,234 number of insertions = 10,209 mapped reads with insertion percentage = 0.4% number of deletions = 62,184 mapped reads with deletion percentage = 2.4% homopolymer indels = 40.35% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.7992X There is a 2.12% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.37% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 16606893 0.06662728836290442 0.7504930220559066 chr2 243199373 11233264 0.04618952697711108 1.5249531545332093 chr3 198022430 8902535 0.04495720510045251 0.4220031525040245 chr4 191154276 5444601 0.028482758083842184 0.3609555897090332 chr5 180915260 5970078 0.0329993058628664 0.36473638179572 chr6 171115067 24805018 0.14496103957929082 1.2531213042295393 chr7 159138663 8077582 0.05075813663207664 0.659345966260878 chr8 146364022 10856230 0.07417280457078448 0.698001545308127 chr9 141213431 5495217 0.03891426588169223 0.7290809511459356 chr10 135534747 4849916 0.035783561834516135 0.47985887094846774 chr11 135006516 4088411 0.03028306426335748 0.5595013407119475 chr12 133851895 6582614 0.049178339985399534 0.49482852310180575 chr13 115169878 4440259 0.03855399586339755 0.4790021342578667 chr14 107349540 5225516 0.04867758166453252 0.49344693383560595 chr15 102531392 4289640 0.04183733309696995 0.43792265489679544 chr16 90354753 3679573 0.04072362413519076 0.5045838623244342 chr17 81195210 4056805 0.04996360006951149 0.43743939718830543 chr18 78077248 2790206 0.03573647985133902 2.2425888766987345 chr19 59128983 2324722 0.039316116767981614 0.7600562977409768 chr20 63025520 2489068 0.03949301806633249 0.41167475103346196 chr21 48129895 2460733 0.05112691394818127 0.46125378315310867 chr22 51304566 1436662 0.028002614815999027 0.313072236742875 chrMT 16571 15466 0.9333172409631284 1.8127373343938937 chrX 155270560 4518442 0.02910044247924397 0.40035527311365565 chrY 59373566 401211 0.006757401096642907 0.31323764237676666