BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867846.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 = 2,380,174 number of mapped reads = 2,190,684 (92.04%) number of supplementary alignments = 9,756 (0.41%) number of secondary alignments = 0 number of mapped bases = 129,081,439 bp number of sequenced bases = 129,042,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,266 duplication rate = 4.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8807 >>>>>>> ACTG content number of A's = 33,536,470 bp (25.99%) number of C's = 24,026,678 bp (18.62%) number of T's = 41,479,125 bp (32.14%) number of G's = 29,983,101 bp (23.24%) number of N's = 16,862 bp (0.01%) GC percentage = 41.85% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 652,339 number of insertions = 10,629 mapped reads with insertion percentage = 0.48% number of deletions = 24,724 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3879X There is a 3.63% of reference with a coverageData >= 1X There is a 0.39% of reference with a coverageData >= 2X There is a 0.06% 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% 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 10385720 0.04166777983674512 0.7208317109415643 chr2 243199373 10918193 0.04489400143313692 0.5401744305077999 chr3 198022430 8477361 0.042810104895692876 0.23106068466416418 chr4 191154276 8309267 0.0434689046663021 0.2817061659875577 chr5 180915260 7808411 0.0431605990561548 0.23533211859047273 chr6 171115067 7407584 0.04329007450875147 0.2723005937724322 chr7 159138663 7116606 0.04471952865407698 0.4665743023835448 chr8 146364022 6647217 0.04541564866262011 0.44882409119274774 chr9 141213431 5411434 0.03832095829468232 0.3079335524387992 chr10 135534747 6266756 0.04623726489857247 0.4022775702935367 chr11 135006516 5877675 0.04353623198453621 0.3163031484441171 chr12 133851895 5783543 0.043208525363051455 0.23663619492052668 chr13 115169878 4042892 0.035103727382606066 0.21676460597868205 chr14 107349540 3890818 0.036244384465923186 0.2225098611611878 chr15 102531392 3715437 0.03623706776554833 0.2158158810475771 chr16 90354753 3705220 0.04100747195889075 0.2520707095847565 chr17 81195210 3507891 0.04320317664059247 0.2577754575249555 chr18 78077248 3456746 0.044273409841494415 0.5811218946492043 chr19 59128983 2690855 0.0455082239449307 0.5317426191113923 chr20 63025520 2730234 0.04331949978357973 0.24200651849049576 chr21 48129895 1682694 0.03496151404444161 0.25527098378854146 chr22 51304566 1529651 0.029815104565936685 0.19360258575744632 chrMT 16571 47717 2.8795486090157505 2.334145272999322 chrX 155270560 7212251 0.046449571638049095 0.27307681748219326 chrY 59373566 459266 0.007735193132917096 0.3210325208203474