BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524628.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 = 2,147,987 number of mapped reads = 2,001,128 (93.16%) number of supplementary alignments = 4,825 (0.22%) number of secondary alignments = 0 number of mapped bases = 116,803,678 bp number of sequenced bases = 116,765,219 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 98,510 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3437 >>>>>>> ACTG content number of A's = 30,007,175 bp (25.7%) number of C's = 21,490,158 bp (18.4%) number of T's = 37,762,176 bp (32.34%) number of G's = 27,504,949 bp (23.56%) number of N's = 761 bp (0%) GC percentage = 41.96% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 548,598 number of insertions = 7,389 mapped reads with insertion percentage = 0.37% number of deletions = 22,458 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.69% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3171X There is a 3.26% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 12790324 0.05131511387488178 0.5667695781699612 chr2 243199373 10055168 0.04134536975142613 0.36136696006699315 chr3 198022430 7223171 0.03647652945173938 0.2170428889783591 chr4 191154276 5085986 0.026606707976545605 0.21821350460468653 chr5 180915260 9623896 0.053195601078648645 0.2599371815146205 chr6 171115067 7249271 0.04236489005377884 0.2527005966424933 chr7 159138663 7017293 0.04409546283545187 0.41947333467097897 chr8 146364022 10131909 0.06922404059106821 0.4129007369744167 chr9 141213431 4079818 0.028891147046770642 0.2754142093422358 chr10 135534747 4868832 0.03592312752094487 0.32527225910462154 chr11 135006516 5717635 0.04235080771953259 0.30033465779802787 chr12 133851895 3542561 0.026466274534252952 0.19021280609050448 chr13 115169878 2769305 0.02404539318865997 0.17617496127533314 chr14 107349540 2123489 0.01978107218717472 0.16841110982285132 chr15 102531392 2903947 0.02832251609341264 0.20099476252826634 chr16 90354753 3340774 0.036973970810367886 0.23019503725028717 chr17 81195210 2454022 0.03022372871503134 0.20556367936837072 chr18 78077248 3030642 0.038815942897987385 0.4637163314252829 chr19 59128983 2177233 0.036821756261223026 0.40338504099482914 chr20 63025520 2100413 0.033326389056369546 0.2126318821463246 chr21 48129895 1014973 0.021088203080434728 0.187217762130949 chr22 51304566 1997570 0.03893552086572567 0.223266572701125 chrMT 16571 3467 0.20922092812745158 0.5666932266174421 chrX 155270560 5230672 0.033687467862549086 0.23789469960657272 chrY 59373566 271307 0.004569491413064191 0.13800901796001075