BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716105.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 = 767,801 number of mapped reads = 695,608 (90.6%) number of supplementary alignments = 2,293 (0.3%) number of secondary alignments = 0 number of mapped bases = 39,743,915 bp number of sequenced bases = 39,731,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,238 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9964 >>>>>>> ACTG content number of A's = 9,359,792 bp (23.56%) number of C's = 6,880,128 bp (17.32%) number of T's = 13,337,173 bp (33.57%) number of G's = 10,153,934 bp (25.56%) number of N's = 787 bp (0%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 208,456 number of insertions = 2,756 mapped reads with insertion percentage = 0.39% number of deletions = 7,611 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.19% >>>>>>> Coverage mean coverageData = 0.0128X std coverageData = 0.1528X There is a 1.21% 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 3300184 0.013240424383937643 0.23145844071137223 chr2 243199373 3170969 0.013038557463715171 0.19336571885882836 chr3 198022430 2343030 0.01183214446969467 0.11457159473189002 chr4 191154276 2520924 0.013187902738832795 0.1251259730165481 chr5 180915260 2279005 0.012597085508430854 0.11706676728449206 chr6 171115067 2150455 0.012567303614473646 0.13058145981000777 chr7 159138663 2282208 0.014341002726659832 0.20001164284025993 chr8 146364022 2148930 0.014682091750662605 0.18386458510211542 chr9 141213431 1314132 0.009305998662407685 0.11421185125310139 chr10 135534747 1745088 0.01287557647486515 0.16203587860654795 chr11 135006516 1420910 0.01052475126459822 0.12362439263313411 chr12 133851895 1978430 0.014780739562932597 0.1269748882825794 chr13 115169878 1210278 0.010508633168822147 0.10704940735253687 chr14 107349540 1335344 0.012439214923510617 0.11727532891464289 chr15 102531392 1448186 0.014124318140535925 0.12458613734928686 chr16 90354753 1312368 0.01452461499175367 0.13074548370039107 chr17 81195210 1661953 0.020468608924097863 0.1514337587878806 chr18 78077248 765931 0.00980991286987984 0.17163724224126956 chr19 59128983 966733 0.016349562447235056 0.1978171995628474 chr20 63025520 1225721 0.019448010900981062 0.14797981694393025 chr21 48129895 499086 0.01036956344907879 0.11178921531486337 chr22 51304566 338603 0.006599860916862643 0.08449042843159348 chrMT 16571 6997 0.42224367871582885 0.7119798878453344 chrX 155270560 2186157 0.01407966197842012 0.13088897719014767 chrY 59373566 132293 0.002228146444833716 0.08605956926686181