BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524771.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 = 1,449,959 number of mapped reads = 1,330,423 (91.76%) number of supplementary alignments = 4,935 (0.34%) number of secondary alignments = 0 number of mapped bases = 77,107,547 bp number of sequenced bases = 77,081,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,231 duplication rate = 2.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7019 >>>>>>> ACTG content number of A's = 18,805,868 bp (24.4%) number of C's = 14,491,122 bp (18.8%) number of T's = 24,634,214 bp (31.96%) number of G's = 19,140,941 bp (24.83%) number of N's = 9,641 bp (0.01%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 389,799 number of insertions = 5,244 mapped reads with insertion percentage = 0.39% number of deletions = 15,845 mapped reads with deletion percentage = 1.18% homopolymer indels = 40.85% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2201X There is a 2.26% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6146553 0.024660131137647194 0.30504739242610823 chr2 243199373 6485496 0.026667404278217444 0.31115758830178203 chr3 198022430 5053183 0.025518235484737764 0.17446370556557714 chr4 191154276 4923500 0.02575668252380606 0.1947150331305546 chr5 180915260 4581170 0.02532218675196332 0.17228420492685154 chr6 171115067 4352495 0.02543607103867715 0.1815602986090753 chr7 159138663 4259428 0.026765513293271793 0.2668116728473789 chr8 146364022 3857839 0.026357836764010215 0.20259590767531502 chr9 141213431 3286871 0.023275909215745915 0.20034256113865878 chr10 135534747 3767901 0.027800258482793345 0.25916016202066394 chr11 135006516 3488233 0.025837515872196865 0.20473310282738574 chr12 133851895 3483957 0.026028447337260334 0.17525286722842126 chr13 115169878 2403086 0.02086557736911035 0.1556801121123072 chr14 107349540 2353348 0.02192229235448983 0.16394562282905867 chr15 102531392 2228099 0.021730895841148824 0.16058302401319982 chr16 90354753 2338432 0.025880564357250804 0.19011448256692487 chr17 81195210 2161817 0.026624932677678893 0.18469227010172612 chr18 78077248 2021083 0.025885684392974506 0.3073177953546586 chr19 59128983 1712980 0.02897022598883529 0.2580246377705604 chr20 63025520 1692706 0.026857469799535173 0.18646858912702652 chr21 48129895 1024061 0.021277025432945573 0.175706293158634 chr22 51304566 967283 0.018853741010108144 0.14993147079057323 chrMT 16571 24837 1.498823245428761 1.5036960878491317 chrX 155270560 4246664 0.02735009135022119 0.19147614092189388 chrY 59373566 246525 0.004152100279777704 0.11791227326661372