BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716124.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 = 2,404,223 number of mapped reads = 2,150,664 (89.45%) number of supplementary alignments = 43,808 (1.82%) number of secondary alignments = 0 number of mapped bases = 169,662,289 bp number of sequenced bases = 169,585,279 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 101,472 duplication rate = 3.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3252 >>>>>>> ACTG content number of A's = 43,657,204 bp (25.74%) number of C's = 32,013,670 bp (18.88%) number of T's = 53,251,807 bp (31.4%) number of G's = 40,650,606 bp (23.97%) number of N's = 11,992 bp (0.01%) GC percentage = 42.85% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,110,459 number of insertions = 15,359 mapped reads with insertion percentage = 0.7% number of deletions = 40,025 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.0548X std coverageData = 0.5112X There is a 4.57% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.12% 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 16953362 0.0680173310380639 1.139734635896756 chr2 243199373 14320149 0.05888234341788373 0.5382204299930936 chr3 198022430 11028738 0.05569438775193295 0.269385002926325 chr4 191154276 10882760 0.05693181563984475 0.3649275544996692 chr5 180915260 10191487 0.0563329317825373 0.273975932721051 chr6 171115067 9581849 0.05599652425697849 0.3010884436912538 chr7 159138663 9114732 0.05727540893063806 0.5845054954702434 chr8 146364022 4619087 0.03155889635227433 0.5235020884062331 chr9 141213431 7005862 0.04961186730177245 0.41475092974968025 chr10 135534747 8057298 0.05944820924777319 0.5069053419128803 chr11 135006516 9713647 0.07194946797975292 0.544324183492003 chr12 133851895 7513680 0.05613428184935297 0.2733156669105347 chr13 115169878 5950528 0.05166739865783308 0.26306714268713827 chr14 107349540 5019381 0.046757359183840004 0.27134495226977967 chr15 102531392 4898790 0.04777844038243429 0.24938020227301458 chr16 90354753 3903173 0.043198314094223686 0.2748270745551784 chr17 81195210 5429461 0.06686922787686614 0.36678823308876357 chr18 78077248 4499052 0.057623086305500934 0.6927045421492349 chr19 59128983 3320307 0.05615362943076494 0.7038462616376422 chr20 63025520 3603397 0.057173617924929455 0.29275849516574864 chr21 48129895 2248681 0.04672108675907147 0.2989588311891569 chr22 51304566 2014975 0.03927476942305681 0.2284864427911631 chrMT 16571 8964 0.5409450244402872 0.8606011168003531 chrX 155270560 9255274 0.05960739756461238 0.3338015319573985 chrY 59373566 527655 0.00888703568857562 0.3055600592681039