BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717047.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 = 786,941 number of mapped reads = 634,736 (80.66%) number of supplementary alignments = 2,472 (0.31%) number of secondary alignments = 0 number of mapped bases = 35,255,649 bp number of sequenced bases = 35,244,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,685 duplication rate = 1.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.7285 >>>>>>> ACTG content number of A's = 8,182,269 bp (23.22%) number of C's = 7,787,360 bp (22.09%) number of T's = 10,575,519 bp (30.01%) number of G's = 8,698,812 bp (24.68%) number of N's = 956 bp (0%) GC percentage = 46.78% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 191,322 number of insertions = 3,037 mapped reads with insertion percentage = 0.47% number of deletions = 6,268 mapped reads with deletion percentage = 0.98% homopolymer indels = 34.55% >>>>>>> Coverage mean coverageData = 0.0114X std coverageData = 0.1269X There is a 1.06% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 3271429 0.013125058573073726 0.14510862787492645 chr2 243199373 2892945 0.011895363726945135 0.15607154912274954 chr3 198022430 2288336 0.011555943435296699 0.11557164817321583 chr4 191154276 2203064 0.011525057383492692 0.1262511153857803 chr5 180915260 2845955 0.01573087311706044 0.13299088106778462 chr6 171115067 1557145 0.00909998767086945 0.10257227323281051 chr7 159138663 1933774 0.01215150337162252 0.13612617253802833 chr8 146364022 2109238 0.014410904887541284 0.13193776512403732 chr9 141213431 1540858 0.010911554156629762 0.11721439563761088 chr10 135534747 1813842 0.013382855984524765 0.17509296753057035 chr11 135006516 1411067 0.010451843672493556 0.12439770780634384 chr12 133851895 1603712 0.011981242402283508 0.11547625149486196 chr13 115169878 588583 0.005110563718752919 0.07590589610982093 chr14 107349540 1512946 0.014093642133911333 0.12705653326506075 chr15 102531392 682522 0.00665671251200803 0.08751115203362997 chr16 90354753 919767 0.010179508763639695 0.11266294541490704 chr17 81195210 1314645 0.0161911644787913 0.1392958143968657 chr18 78077248 884573 0.011329459255531138 0.13364143102742498 chr19 59128983 962972 0.016285955738491224 0.15236092807669285 chr20 63025520 857007 0.013597777535195267 0.12821693758172176 chr21 48129895 481281 0.009999627050921263 0.11274082739187376 chr22 51304566 373516 0.0072803656501060745 0.09216127288616364 chrMT 16571 6299 0.3801218997043027 0.6797879882338091 chrX 155270560 1079071 0.006949617493490073 0.094802331990588 chrY 59373566 121102 0.002039661892634173 0.07254225595869031