BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716253.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 = 2,192,555 number of mapped reads = 2,046,258 (93.33%) number of supplementary alignments = 40,182 (1.83%) number of secondary alignments = 0 number of mapped bases = 158,933,989 bp number of sequenced bases = 158,873,614 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,751 duplication rate = 4.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4517 >>>>>>> ACTG content number of A's = 40,640,103 bp (25.58%) number of C's = 32,325,923 bp (20.35%) number of T's = 46,144,466 bp (29.04%) number of G's = 39,757,135 bp (25.02%) number of N's = 5,987 bp (0%) GC percentage = 45.37% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,037,644 number of insertions = 14,617 mapped reads with insertion percentage = 0.7% number of deletions = 28,950 mapped reads with deletion percentage = 1.39% homopolymer indels = 38.77% >>>>>>> Coverage mean coverageData = 0.0513X std coverageData = 0.4142X There is a 4.11% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17707663 0.07104360634672201 0.7957302057527084 chr2 243199373 14828488 0.06097255851066689 0.4499932668960271 chr3 198022430 10232607 0.05167397955878029 0.27412962289913584 chr4 191154276 7749038 0.040538135803982744 0.3579194093962328 chr5 180915260 8158506 0.04509573155962631 0.2572563855459264 chr6 171115067 9721606 0.05681326706315114 0.30996221670115676 chr7 159138663 10024884 0.0629946476300357 0.534512118914362 chr8 146364022 9867388 0.06741675901745854 0.4464340740233475 chr9 141213431 4815945 0.03410401521934553 0.2976066532430879 chr10 135534747 8157795 0.06018969438147105 0.5591166331234338 chr11 135006516 4708852 0.03487870170651615 0.2986239700976874 chr12 133851895 5851983 0.043719836764358096 0.2518429796972728 chr13 115169878 2982675 0.025898047751687296 0.19002318967940526 chr14 107349540 3058775 0.028493601369880113 0.2236665438277583 chr15 102531392 3272441 0.03191647880875352 0.2126665090361673 chr16 90354753 4891383 0.054135314829536416 0.3045263935664443 chr17 81195210 4023823 0.04955739384133621 0.2977346465395854 chr18 78077248 4637679 0.059398597143177995 0.43593506797361053 chr19 59128983 4054688 0.06857361304523028 0.603996815279149 chr20 63025520 4350675 0.06903037055465785 0.3406263007138198 chr21 48129895 2485066 0.051632483303776164 0.3409384476309925 chr22 51304566 2570214 0.05009717848504946 0.28029038576149745 chrMT 16571 58752 3.545471003560437 3.355159323289852 chrX 155270560 10183843 0.0655877263532765 0.329774414659799 chrY 59373566 539220 0.009081819340276782 0.29668594585634706