BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524682.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 = 2,254,908 number of mapped reads = 2,091,475 (92.75%) number of supplementary alignments = 9,523 (0.42%) number of secondary alignments = 0 number of mapped bases = 123,623,422 bp number of sequenced bases = 123,585,728 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,609 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7379 >>>>>>> ACTG content number of A's = 32,164,685 bp (26.03%) number of C's = 24,178,367 bp (19.56%) number of T's = 38,531,132 bp (31.18%) number of G's = 28,694,538 bp (23.22%) number of N's = 17,006 bp (0.01%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 613,149 number of insertions = 8,647 mapped reads with insertion percentage = 0.41% number of deletions = 23,493 mapped reads with deletion percentage = 1.11% homopolymer indels = 43.34% >>>>>>> Coverage mean coverageData = 0.0399X std coverageData = 0.3509X There is a 3.5% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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% 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 9952285 0.03992882729868906 0.6177127737858974 chr2 243199373 10452194 0.042977882183931455 0.480184268606031 chr3 198022430 8127672 0.04104419888191454 0.22646065517743721 chr4 191154276 7947431 0.04157600429508571 0.268783594092781 chr5 180915260 7426387 0.04104898061114358 0.2270074039901693 chr6 171115067 7127344 0.04165234613735096 0.25819031375288 chr7 159138663 6778809 0.042596870378381904 0.41255653477521015 chr8 146364022 6248886 0.04269413968413631 0.39383505918960005 chr9 141213431 5235059 0.03707196236879196 0.2940106809961782 chr10 135534747 5955342 0.04393959579973983 0.37134834269858347 chr11 135006516 5561520 0.04119445612536213 0.30382444025254557 chr12 133851895 5647063 0.042188890938002786 0.23138208664146456 chr13 115169878 3896764 0.033834923398981115 0.2048874192709683 chr14 107349540 3700906 0.0344752851293075 0.21742079540337206 chr15 102531392 3568006 0.03479915692551994 0.2103786425768232 chr16 90354753 3598992 0.03983179501359491 0.24081251928055064 chr17 81195210 3358552 0.041363917896141904 0.24497338970021038 chr18 78077248 3256720 0.04171151114342555 0.5419821027385124 chr19 59128983 2607839 0.044104242415263596 0.48972132674632046 chr20 63025520 2652404 0.04208460318931125 0.23518419214100336 chr21 48129895 1617750 0.03361216557817132 0.2378541998720639 chr22 51304566 1464338 0.02854205997961273 0.18947982637183053 chrMT 16571 102659 6.195099873272585 4.101855201573685 chrX 155270560 6936346 0.04467264109822235 0.2639959901669267 chrY 59373566 402154 0.006773283585493248 0.2391207080329276