BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237584.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,918,513 number of mapped reads = 1,557,287 (81.17%) number of supplementary alignments = 9,798 (0.51%) number of secondary alignments = 0 number of mapped bases = 98,284,557 bp number of sequenced bases = 98,230,105 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,377 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7686 >>>>>>> ACTG content number of A's = 25,327,968 bp (25.78%) number of C's = 18,912,127 bp (19.25%) number of T's = 29,338,044 bp (29.87%) number of G's = 24,634,420 bp (25.08%) number of N's = 17,546 bp (0.02%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 908,873 number of insertions = 9,247 mapped reads with insertion percentage = 0.59% number of deletions = 33,190 mapped reads with deletion percentage = 2.1% homopolymer indels = 45.58% >>>>>>> Coverage mean coverageData = 0.0317X std coverageData = 0.2978X There is a 2.65% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 8505796 0.03412547565929635 0.3956873224914108 chr2 243199373 8667144 0.035638019510847996 0.4202801934548717 chr3 198022430 6744974 0.034061666650591044 0.22869624202515543 chr4 191154276 5513639 0.02884392185922119 0.23601216646338685 chr5 180915260 5524683 0.030537407402780728 0.21004266569861121 chr6 171115067 5512337 0.032214211738584075 0.2422092968950272 chr7 159138663 5761431 0.03620384192872099 0.42243474399161485 chr8 146364022 4911137 0.033554263765722424 0.2739329424953487 chr9 141213431 4196781 0.029719418119654638 0.30543649801939976 chr10 135534747 4629925 0.03416042824796803 0.3201895055572592 chr11 135006516 4084055 0.03025079915402009 0.30855350398720527 chr12 133851895 5538734 0.041379571055008224 0.26130102849301323 chr13 115169878 3166949 0.027498066812226718 0.20705023015731291 chr14 107349540 2753650 0.02565125104401938 0.2319145702985632 chr15 102531392 2775348 0.027068275831074254 0.2101162174526353 chr16 90354753 2723435 0.03014157982369782 0.24529141661780013 chr17 81195210 2513072 0.03095098836495404 0.23524521284201785 chr18 78077248 2275457 0.029143662952874568 0.4230785787636468 chr19 59128983 2152226 0.036398833377533316 0.3324424200430048 chr20 63025520 2081793 0.03303095317579292 0.22784412670620358 chr21 48129895 1290951 0.026822227640430133 0.2329734487008691 chr22 51304566 1050799 0.020481588324906597 0.17885753936476237 chrMT 16571 85951 5.186832418079778 4.367668298453275 chrX 155270560 5456946 0.03514475635303949 0.2462302937379977 chrY 59373566 367344 0.006186995741505572 0.1617001178752745