BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238067.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,675,794 number of mapped reads = 1,546,478 (92.28%) number of supplementary alignments = 11,732 (0.7%) number of secondary alignments = 0 number of mapped bases = 104,576,530 bp number of sequenced bases = 104,530,894 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,010 duplication rate = 2.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.684 >>>>>>> ACTG content number of A's = 29,178,697 bp (27.91%) number of C's = 19,361,930 bp (18.52%) number of T's = 33,195,236 bp (31.76%) number of G's = 22,781,342 bp (21.79%) number of N's = 13,689 bp (0.01%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 755,504 number of insertions = 7,444 mapped reads with insertion percentage = 0.48% number of deletions = 25,605 mapped reads with deletion percentage = 1.64% homopolymer indels = 47.27% >>>>>>> Coverage mean coverageData = 0.0338X std coverageData = 0.3493X There is a 2.94% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% 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% 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 6076726 0.024379983390292136 0.6816148050568185 chr2 243199373 9295040 0.03821983537761835 0.3709896540829717 chr3 198022430 10859308 0.054838777607162985 0.2606544375152878 chr4 191154276 5552862 0.02904911214227821 0.19734805486644788 chr5 180915260 4776029 0.026399260073473072 0.1829363144295599 chr6 171115067 7869946 0.04599212762485726 0.2829594098224408 chr7 159138663 4698889 0.029527010667420275 0.3990416008091097 chr8 146364022 6498383 0.04439877308099664 0.5618140257287891 chr9 141213431 3756804 0.02660373006587454 0.3116569318989307 chr10 135534747 4426294 0.03265800171523543 0.30661777240887755 chr11 135006516 3493694 0.025877965771666903 0.23478443133364593 chr12 133851895 4263521 0.031852526256725765 0.20395100681507664 chr13 115169878 4500599 0.039077917578414036 0.21945228231524358 chr14 107349540 3512698 0.03272205917230758 0.216112045715119 chr15 102531392 3088920 0.030126578209335148 0.19354899327283398 chr16 90354753 3658174 0.04048679099371784 0.2528835711553479 chr17 81195210 2758123 0.03396903585814976 0.22052247372188713 chr18 78077248 3619373 0.04635630856251491 0.5930679433728754 chr19 59128983 2293944 0.03879559369387429 0.4297889230014772 chr20 63025520 2377323 0.03772000611815658 0.22164038613670825 chr21 48129895 1237696 0.025715742783149642 0.1935463159882632 chr22 51304566 1261279 0.024584147149787797 0.1729231357116224 chrMT 16571 44088 2.6605515659887757 2.252890187058947 chrX 155270560 4404656 0.028367618433268998 0.20870714379148084 chrY 59373566 252161 0.0042470246776149505 0.10539747900744333