BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716319.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 = 460,998 number of mapped reads = 422,713 (91.7%) number of supplementary alignments = 2,049 (0.44%) number of secondary alignments = 0 number of mapped bases = 24,582,916 bp number of sequenced bases = 24,576,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,935 duplication rate = 1.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8477 >>>>>>> ACTG content number of A's = 5,955,610 bp (24.23%) number of C's = 4,590,254 bp (18.68%) number of T's = 7,910,524 bp (32.19%) number of G's = 6,119,170 bp (24.9%) number of N's = 646 bp (0%) GC percentage = 43.58% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 120,723 number of insertions = 1,383 mapped reads with insertion percentage = 0.33% number of deletions = 4,307 mapped reads with deletion percentage = 1.01% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.0079X std coverageData = 0.1063X There is a 0.76% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 2688741 0.010787299101653993 0.16608527802235132 chr2 243199373 2158206 0.008874225181493375 0.12182426782970608 chr3 198022430 2258234 0.011403930352738324 0.11015797475139279 chr4 191154276 1154336 0.006038766299949262 0.08119557261749016 chr5 180915260 1109891 0.0061348666773604395 0.080467163508004 chr6 171115067 1673658 0.009780892059025988 0.1144668320496657 chr7 159138663 1435139 0.009018166754360629 0.1193542686382259 chr8 146364022 1799961 0.012297837784206286 0.1180347436662423 chr9 141213431 917963 0.006500536057366951 0.09176221821929195 chr10 135534747 1128348 0.008325156647837326 0.11359561692472511 chr11 135006516 833688 0.006175168611861667 0.08925278515504488 chr12 133851895 1102666 0.00823795583917583 0.09400114588132248 chr13 115169878 622803 0.005407690021170293 0.07599786850217963 chr14 107349540 549807 0.005121652128178659 0.07538581038512121 chr15 102531392 742139 0.007238163703073494 0.0873811566385586 chr16 90354753 521390 0.005770476734079501 0.08155524586445603 chr17 81195210 534773 0.006586262908858786 0.08406055189047154 chr18 78077248 489919 0.006274798517488731 0.12135679783741551 chr19 59128983 467776 0.007911111882306516 0.11759714694382373 chr20 63025520 367332 0.0058283057402779065 0.07838563769468523 chr21 48129895 227888 0.004734853462697145 0.07236070945657723 chr22 51304566 390181 0.007605190539960907 0.08948028134423278 chrMT 16571 541 0.032647396053346205 0.19363752124681582 chrX 155270560 1344081 0.008656380192098231 0.09974420364978835 chrY 59373566 63455 0.0010687416012708417 0.03824075498455629