BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716374.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 = 2,070,991 number of mapped reads = 1,959,947 (94.64%) number of supplementary alignments = 39,557 (1.91%) number of secondary alignments = 0 number of mapped bases = 156,056,955 bp number of sequenced bases = 155,987,052 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,645 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5467 >>>>>>> ACTG content number of A's = 40,788,145 bp (26.15%) number of C's = 30,543,521 bp (19.58%) number of T's = 46,180,094 bp (29.61%) number of G's = 38,464,903 bp (24.66%) number of N's = 10,389 bp (0.01%) GC percentage = 44.24% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 956,251 number of insertions = 12,585 mapped reads with insertion percentage = 0.63% number of deletions = 35,885 mapped reads with deletion percentage = 1.8% homopolymer indels = 43.37% >>>>>>> Coverage mean coverageData = 0.0504X std coverageData = 0.4663X There is a 4.23% of reference with a coverageData >= 1X There is a 0.56% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 15239960 0.06114311747291494 1.0049330065627677 chr2 243199373 12879490 0.05295856581011827 0.4834506732314575 chr3 198022430 9828102 0.04963125641878044 0.25368687855572203 chr4 191154276 9788236 0.051205948435074505 0.34610740310399696 chr5 180915260 8990560 0.04969486819409264 0.2551790990112814 chr6 171115067 8479022 0.04955158039940457 0.27640674578524005 chr7 159138663 8156530 0.05125423229174673 0.5495418286843292 chr8 146364022 7790781 0.05322879826300483 0.5169730831765565 chr9 141213431 6404773 0.045355267941899945 0.37978479164053464 chr10 135534747 7269647 0.05363677699564378 0.46265214707795216 chr11 135006516 8703299 0.06446576993365269 0.49656547389245614 chr12 133851895 6712777 0.05015078045775893 0.2561215473420117 chr13 115169878 5236723 0.04546955411379354 0.24375491912538821 chr14 107349540 4583367 0.0426957302285599 0.2574236661839412 chr15 102531392 4291093 0.04185150436658463 0.23092149758256125 chr16 90354753 3532526 0.039096183462534614 0.2546085867366295 chr17 81195210 5006806 0.06166380997105617 0.3512176991209708 chr18 78077248 4023718 0.051535089966285696 0.6397680599322396 chr19 59128983 3063705 0.05181393023451798 0.6636069313551504 chr20 63025520 3311697 0.052545334017077526 0.28015555601750913 chr21 48129895 2053639 0.042668678167695984 0.28937709313355037 chr22 51304566 1838263 0.03583039762971584 0.21652276614683375 chrMT 16571 91437 5.5178927041216586 3.725996767022377 chrX 155270560 8288707 0.05338234756157252 0.3122158194874747 chrY 59373566 492097 0.008288149645584704 0.2846437971550622