BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717022.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 = 3,015,658 number of mapped reads = 2,652,012 (87.94%) number of supplementary alignments = 14,987 (0.5%) number of secondary alignments = 0 number of mapped bases = 149,988,870 bp number of sequenced bases = 149,949,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,539 duplication rate = 2.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2014 >>>>>>> ACTG content number of A's = 38,185,068 bp (25.47%) number of C's = 30,452,126 bp (20.31%) number of T's = 45,598,027 bp (30.41%) number of G's = 35,711,377 bp (23.82%) number of N's = 3,205 bp (0%) GC percentage = 44.12% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 741,072 number of insertions = 10,317 mapped reads with insertion percentage = 0.39% number of deletions = 23,104 mapped reads with deletion percentage = 0.87% homopolymer indels = 40.66% >>>>>>> Coverage mean coverageData = 0.0485X std coverageData = 0.3433X There is a 4.17% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 16551321 0.06640433204778254 0.4844469035921492 chr2 243199373 12688283 0.052172350789736616 0.4287441815143033 chr3 198022430 9778102 0.04937875976978971 0.25437097750075965 chr4 191154276 9658984 0.05052978255113686 0.2951430014925018 chr5 180915260 7207626 0.03983979018685323 0.23282154166098185 chr6 171115067 7873070 0.04601038434564035 0.2667933878048824 chr7 159138663 6487858 0.040768584313165934 0.305486565921398 chr8 146364022 9336383 0.06378878410433406 0.34197805310361307 chr9 141213431 5494073 0.03890616466927994 0.37195283449193867 chr10 135534747 7157510 0.05280940982610164 0.4396744804638777 chr11 135006516 4761854 0.0352712901649873 0.316141076354778 chr12 133851895 6774143 0.05060924240183525 0.2621933477870008 chr13 115169878 4678878 0.04062588309766205 0.22573990463276855 chr14 107349540 5347589 0.04981473604824017 0.2880028036681677 chr15 102531392 4322005 0.04215299251959829 0.23340355428149342 chr16 90354753 4422262 0.048943324542096864 0.2909381057357382 chr17 81195210 3372003 0.041529580377955795 0.2425759024276929 chr18 78077248 3666954 0.04696571784907173 0.6877930499899125 chr19 59128983 2924962 0.0494674836534902 0.39885172967022325 chr20 63025520 4778555 0.07581936650423511 0.33443645961942897 chr21 48129895 1978629 0.04111018733782818 0.2643641349711694 chr22 51304566 1780380 0.03470217446143098 0.21175776533988785 chrMT 16571 23246 1.4028121416933197 1.4687510289007963 chrX 155270560 8477309 0.054597014398608465 0.3180082885557392 chrY 59373566 446891 0.007526767046466436 0.17344960179991528