BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716907.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 = 3,157,911 number of mapped reads = 2,922,233 (92.54%) number of supplementary alignments = 19,678 (0.62%) number of secondary alignments = 0 number of mapped bases = 170,422,234 bp number of sequenced bases = 170,373,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,145 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7578 >>>>>>> ACTG content number of A's = 42,432,625 bp (24.91%) number of C's = 34,869,872 bp (20.47%) number of T's = 51,535,443 bp (30.25%) number of G's = 41,533,563 bp (24.38%) number of N's = 2,218 bp (0%) GC percentage = 44.84% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 845,666 number of insertions = 10,189 mapped reads with insertion percentage = 0.35% number of deletions = 30,434 mapped reads with deletion percentage = 1.03% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 0.4151X There is a 4.48% of reference with a coverageData >= 1X There is a 0.73% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% 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% 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 13801776 0.05537308571038625 0.677677395919435 chr2 243199373 14327132 0.05891105648533066 0.5550771156255391 chr3 198022430 11309102 0.057110207161885654 0.28551749942854293 chr4 191154276 10728557 0.05612512167920324 0.33238408931002505 chr5 180915260 10110641 0.05588605958391791 0.28257823092609097 chr6 171115067 9713464 0.056765685046308634 0.3226820336178857 chr7 159138663 9335585 0.05866321121473793 0.5583070385189666 chr8 146364022 8607246 0.058807115863487275 0.438496592019039 chr9 141213431 7089225 0.05020220066744218 0.33925057921677454 chr10 135534747 8151970 0.06014671647264004 0.4339177250557357 chr11 135006516 7761288 0.057488247456145 0.38870584624091037 chr12 133851895 7741075 0.05783313714012043 0.2942195099596247 chr13 115169878 5192600 0.04508644178645392 0.2548959210773519 chr14 107349540 5177819 0.048233266765744874 0.27828117265425417 chr15 102531392 5044825 0.049202735880148785 0.27364444842584784 chr16 90354753 5108791 0.056541474912780734 0.31194390550438456 chr17 81195210 4838494 0.05959087980682604 0.330567118876275 chr18 78077248 4463290 0.05716505274366228 0.6339411514549604 chr19 59128983 3700061 0.0625760974106387 0.5281593608061449 chr20 63025520 3748680 0.0594787635230935 0.3040647213844101 chr21 48129895 2216562 0.04605374684486638 0.2960866231107616 chr22 51304566 2198982 0.04286133128969457 0.25003459295045144 chrMT 16571 34078 2.0564842194194677 1.967988758346058 chrX 155270560 9514700 0.0612781972319801 0.3342676464677529 chrY 59373566 506291 0.008527212261429606 0.22301920557451865