BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008781.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 = 1,363,162 number of mapped reads = 1,122,236 (82.33%) number of supplementary alignments = 6,929 (0.51%) number of secondary alignments = 0 number of mapped bases = 74,077,865 bp number of sequenced bases = 74,038,631 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,375 duplication rate = 3.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0471 >>>>>>> ACTG content number of A's = 19,828,197 bp (26.78%) number of C's = 14,365,618 bp (19.4%) number of T's = 22,758,291 bp (30.74%) number of G's = 16,979,495 bp (22.93%) number of N's = 107,030 bp (0.14%) GC percentage = 42.34% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 626,635 number of insertions = 5,373 mapped reads with insertion percentage = 0.47% number of deletions = 22,072 mapped reads with deletion percentage = 1.95% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.0239X std coverageData = 0.2397X There is a 1.93% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 7353852 0.02950384625119951 0.3782514284581163 chr2 243199373 6392583 0.02628535970773247 0.32999506118350636 chr3 198022430 5777118 0.029174058716479743 0.20995520761716863 chr4 191154276 3574668 0.018700434407232406 0.16834917958900467 chr5 180915260 2543664 0.014059974819150138 0.14016051467476162 chr6 171115067 3659441 0.02138584909065898 0.19230582152576411 chr7 159138663 3459707 0.02174020401315047 0.22314857975975902 chr8 146364022 5733932 0.03917582969945989 0.2926267834273849 chr9 141213431 2294832 0.016250805491724085 0.17642428495339554 chr10 135534747 4413443 0.03256318470126336 0.332095621299294 chr11 135006516 2700360 0.020001701251219608 0.1870281619486333 chr12 133851895 2945559 0.022006106077168353 0.17759164151748774 chr13 115169878 1646386 0.01429528300794067 0.14288835561065152 chr14 107349540 2747330 0.02559237794591388 0.19427188945886373 chr15 102531392 1847061 0.018014590107193706 0.16067125276905253 chr16 90354753 2258418 0.024995010500443733 0.2296774867626276 chr17 81195210 2680908 0.03301805611439394 0.23302402221987178 chr18 78077248 1346631 0.017247418863943566 0.264344984929173 chr19 59128983 2043297 0.03455660652915339 0.2954397140642554 chr20 63025520 1961748 0.031126248541860503 0.21517663191314168 chr21 48129895 913015 0.018969810758988775 0.17308764005975832 chr22 51304566 1081124 0.021072666319796957 0.17377916958628728 chrMT 16571 86772 5.2363768028483495 3.92821519774304 chrX 155270560 4399319 0.028333246173646826 0.20709189384910412 chrY 59373566 216697 0.003649721830755458 0.10965495602492624