BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524366.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 = 1,240,568 number of mapped reads = 1,138,076 (91.74%) number of supplementary alignments = 4,474 (0.36%) number of secondary alignments = 0 number of mapped bases = 66,088,670 bp number of sequenced bases = 66,066,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,262 duplication rate = 2.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5602 >>>>>>> ACTG content number of A's = 16,491,746 bp (24.96%) number of C's = 12,081,247 bp (18.29%) number of T's = 21,507,024 bp (32.55%) number of G's = 15,984,722 bp (24.2%) number of N's = 1,408 bp (0%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 335,778 number of insertions = 4,699 mapped reads with insertion percentage = 0.41% number of deletions = 14,104 mapped reads with deletion percentage = 1.23% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.22X There is a 1.96% of reference with a coverageData >= 1X There is a 0.13% 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 5328382 0.02137760772118598 0.36963884079449394 chr2 243199373 5588320 0.022978348714739492 0.3019219974422082 chr3 198022430 4398405 0.022211650468080813 0.15992199097389184 chr4 191154276 4309280 0.02254346640929968 0.17008498141536407 chr5 180915260 3994662 0.022080293282059234 0.15968218216164023 chr6 171115067 3809699 0.022263959958593243 0.17265350743497027 chr7 159138663 3716306 0.02335262801598377 0.2980185016169734 chr8 146364022 3352483 0.022905103004070223 0.22731363282724487 chr9 141213431 2774612 0.019648357669321128 0.18492830201725122 chr10 135534747 3211904 0.023698011551237116 0.21010585486191663 chr11 135006516 2985811 0.022116051050454482 0.18474352848868236 chr12 133851895 2979352 0.022258571684771442 0.1611793024213555 chr13 115169878 2110638 0.018326302299286973 0.14518081317041118 chr14 107349540 2031408 0.0189233041892867 0.14939917710612452 chr15 102531392 1834762 0.017894636600661776 0.1443439616728579 chr16 90354753 1898744 0.021014323397021514 0.17085113976521027 chr17 81195210 1741452 0.02144771840604883 0.16069923825702565 chr18 78077248 1749519 0.02240753926162971 0.3025542164391308 chr19 59128983 1319629 0.022317803098355335 0.2776458937406712 chr20 63025520 1400710 0.022224489381444217 0.16253843491630085 chr21 48129895 849739 0.017655118507946047 0.15020200866552844 chr22 51304566 754507 0.014706429833165337 0.12959291277066798 chrMT 16571 10448 0.6304990646309818 0.8994062897606375 chrX 155270560 3732397 0.024038021116172956 0.17944143824201425 chrY 59373566 205501 0.003461153065995733 0.09970582491291355