BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716561.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 = 4,470,451 number of mapped reads = 4,058,506 (90.79%) number of supplementary alignments = 16,571 (0.37%) number of secondary alignments = 0 number of mapped bases = 231,607,947 bp number of sequenced bases = 231,547,250 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,467 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3043 >>>>>>> ACTG content number of A's = 58,164,529 bp (25.12%) number of C's = 48,528,938 bp (20.96%) number of T's = 68,958,806 bp (29.78%) number of G's = 55,889,833 bp (24.14%) number of N's = 5,144 bp (0%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,122,425 number of insertions = 15,763 mapped reads with insertion percentage = 0.39% number of deletions = 35,768 mapped reads with deletion percentage = 0.88% homopolymer indels = 40.11% >>>>>>> Coverage mean coverageData = 0.0748X std coverageData = 0.4993X There is a 6.01% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 18658255 0.07485740627302188 0.8663338003056269 chr2 243199373 19607128 0.08062162232630427 0.5932637425915558 chr3 198022430 15096157 0.0762345811027569 0.3358033295884525 chr4 191154276 14816775 0.07751212952202022 0.3904975862854645 chr5 180915260 13803747 0.07629951724359792 0.3416267051242248 chr6 171115067 13298550 0.07771700197505109 0.3722871502056382 chr7 159138663 12632473 0.0793802886228848 0.4904427236860676 chr8 146364022 11649878 0.07959523003542496 0.4456300955575505 chr9 141213431 9803666 0.06942445864090648 0.5132582147158911 chr10 135534747 11118735 0.08203604792208746 0.48944657379008166 chr11 135006516 10603449 0.07854027578935524 0.4935616883562985 chr12 133851895 10632303 0.07943333936363023 0.34850067947617475 chr13 115169878 7239408 0.06285851930832123 0.30070159282195275 chr14 107349540 7076686 0.06592190334490487 0.3521341122025253 chr15 102531392 6792722 0.06625016853375013 0.3162329469096975 chr16 90354753 6818247 0.07546085594412504 0.38497431958770206 chr17 81195210 6491207 0.07994568891440763 0.36567606278999626 chr18 78077248 6124968 0.07844753954442657 1.0260579283320197 chr19 59128983 4882585 0.0825751560787034 0.6116288270222476 chr20 63025520 5057911 0.0802517932418487 0.3642872337640435 chr21 48129895 3041192 0.06318717296183589 0.37158535195097003 chr22 51304566 2768636 0.05396470949583708 0.2807927735038537 chrMT 16571 203941 12.307102769899222 7.416616179500704 chrX 155270560 12726596 0.0819639988417637 0.4263142940749971 chrY 59373566 662732 0.01116207168691872 0.22789351312611347