BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716433.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 = 1,481,324 number of mapped reads = 728,126 (49.15%) number of supplementary alignments = 1,985 (0.13%) number of secondary alignments = 0 number of mapped bases = 39,716,588 bp number of sequenced bases = 39,705,314 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,047 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1308 >>>>>>> ACTG content number of A's = 9,711,042 bp (24.46%) number of C's = 7,151,240 bp (18.01%) number of T's = 13,114,946 bp (33.03%) number of G's = 9,727,491 bp (24.5%) number of N's = 595 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 208,475 number of insertions = 2,694 mapped reads with insertion percentage = 0.37% number of deletions = 7,218 mapped reads with deletion percentage = 0.98% homopolymer indels = 40.23% >>>>>>> Coverage mean coverageData = 0.0128X std coverageData = 0.1534X There is a 1.2% of reference with a coverageData >= 1X There is a 0.06% 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 3340109 0.01340060452647779 0.15702915174685922 chr2 243199373 4002710 0.016458553945367285 0.253385600167812 chr3 198022430 3005198 0.015176048491072451 0.13373862889413848 chr4 191154276 2311107 0.01209027100183728 0.11732834963485347 chr5 180915260 2049296 0.011327380564801443 0.1122706377918609 chr6 171115067 2295852 0.01341700669760425 0.13576507857857348 chr7 159138663 2028888 0.012749183396117887 0.26561458606545185 chr8 146364022 2674654 0.018273985392393766 0.15249093066005162 chr9 141213431 1701567 0.012049611626531474 0.12429892624255974 chr10 135534747 1912639 0.014111798209207563 0.17351453288334653 chr11 135006516 1212231 0.008979055499810097 0.10907898383487775 chr12 133851895 1901183 0.01420363155859691 0.12784912296023407 chr13 115169878 1072983 0.009316524586402706 0.10257905188335319 chr14 107349540 1304140 0.01214853831697835 0.11646607313552189 chr15 102531392 987356 0.009629792210370068 0.10750734245645471 chr16 90354753 1255017 0.013889883579229085 0.12778219826494833 chr17 81195210 1532226 0.018870891521802824 0.1466468710864779 chr18 78077248 936983 0.012000717545782351 0.15825375119298393 chr19 59128983 833818 0.014101680050881308 0.1619148872245226 chr20 63025520 911057 0.014455366651477052 0.1276684340148048 chr21 48129895 303217 0.006299972189841677 0.08518504623324726 chr22 51304566 580914 0.01132285184909273 0.11233726983266965 chrMT 16571 4689 0.2829642145917567 0.5512613964013973 chrX 155270560 1468041 0.009454728571855475 0.1143229165867818 chrY 59373566 90713 0.0015278347943594966 0.0465566573283354