BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717039.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 = 1,350,440 number of mapped reads = 1,201,627 (88.98%) number of supplementary alignments = 32,764 (2.43%) number of secondary alignments = 0 number of mapped bases = 88,183,638 bp number of sequenced bases = 88,152,815 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,140 duplication rate = 1.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0422 >>>>>>> ACTG content number of A's = 23,392,332 bp (26.54%) number of C's = 18,031,320 bp (20.45%) number of T's = 26,346,204 bp (29.89%) number of G's = 20,372,827 bp (23.11%) number of N's = 10,132 bp (0.01%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 634,774 number of insertions = 7,919 mapped reads with insertion percentage = 0.65% number of deletions = 17,876 mapped reads with deletion percentage = 1.47% homopolymer indels = 38.17% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2376X There is a 2.59% of reference with a coverageData >= 1X There is a 0.19% 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 9055887 0.03633245511552808 0.3345670173103163 chr2 243199373 8002254 0.03290408976506695 0.3301310966932309 chr3 198022430 6216709 0.03139396380500936 0.19109810536815247 chr4 191154276 3565481 0.018652373750718505 0.16005724258361778 chr5 180915260 4965189 0.027444832459130312 0.1778465071178267 chr6 171115067 5275648 0.030830996314310532 0.19831167425706386 chr7 159138663 4846442 0.030454208352875253 0.3061447440861033 chr8 146364022 5927050 0.04049526597458493 0.2924211080058919 chr9 141213431 4560404 0.032294406896749075 0.23326127805785404 chr10 135534747 5098954 0.03762100946704095 0.29617716613078726 chr11 135006516 3647681 0.02701855516366336 0.21960910224523092 chr12 133851895 3560348 0.026599160213607736 0.17642312617216402 chr13 115169878 2728655 0.023692436315683168 0.16445334175407195 chr14 107349540 2164711 0.0201650701064951 0.1649715971968049 chr15 102531392 1703817 0.01661751554099646 0.14281783282120789 chr16 90354753 2329028 0.0257764857151455 0.18840478727745655 chr17 81195210 2644188 0.032565812687718895 0.2070612499276991 chr18 78077248 2024401 0.025928180767846736 0.30627566866400996 chr19 59128983 1541932 0.02607743143493606 0.27226898978345043 chr20 63025520 1631702 0.025889544425813545 0.1776497260509768 chr21 48129895 1528983 0.03176784408110593 0.19962475314985578 chr22 51304566 1218416 0.023748685448386795 0.16660690597952837 chrMT 16571 3130 0.18888419528091244 0.5586041979587275 chrX 155270560 3702214 0.023843631400569432 0.18228984050661015 chrY 59373566 240414 0.0040491756887231604 0.1226496331320902