BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013193.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 = 1,749,502 number of mapped reads = 1,474,896 (84.3%) number of supplementary alignments = 13,521 (0.77%) number of secondary alignments = 0 number of mapped bases = 95,479,550 bp number of sequenced bases = 95,429,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,880 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8917 >>>>>>> ACTG content number of A's = 25,690,693 bp (26.92%) number of C's = 17,322,992 bp (18.15%) number of T's = 30,702,233 bp (32.17%) number of G's = 21,712,736 bp (22.75%) number of N's = 1,223 bp (0%) GC percentage = 40.91% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 759,313 number of insertions = 7,024 mapped reads with insertion percentage = 0.47% number of deletions = 28,473 mapped reads with deletion percentage = 1.91% homopolymer indels = 45.68% >>>>>>> Coverage mean coverageData = 0.0308X std coverageData = 0.3265X There is a 2.35% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5473234 0.021958757727628692 0.43579181801908884 chr2 243199373 7754505 0.031885382368975104 0.42810569271723004 chr3 198022430 5639514 0.028479167738725355 0.21061282120193042 chr4 191154276 7429132 0.03886458705218815 0.25319024144175173 chr5 180915260 3483805 0.01925655690957192 0.177697757676609 chr6 171115067 2697384 0.015763568032264513 0.1822333144362824 chr7 159138663 5770081 0.03625819704165794 0.40916022432771754 chr8 146364022 4190205 0.02862865438338392 0.4607848212938098 chr9 141213431 2867470 0.02030592968171703 0.34802349347550604 chr10 135534747 4552692 0.033590589135050364 0.29878435315172064 chr11 135006516 2685598 0.019892358380687345 0.23587064231303917 chr12 133851895 6080018 0.045423473459228945 0.2728091944787859 chr13 115169878 671755 0.005832731714797857 0.09455439625816163 chr14 107349540 5700801 0.05310503426470202 0.29941776650563584 chr15 102531392 5250339 0.05120713663967422 0.28543249229252776 chr16 90354753 7196785 0.07965032011099626 0.3705901785665045 chr17 81195210 3312564 0.04079752980502175 0.2589682867313867 chr18 78077248 2994773 0.03835653889850216 0.6336825392425125 chr19 59128983 2982801 0.05044566722887826 0.5219839121317055 chr20 63025520 2732449 0.04335464427742921 0.26608951503510986 chr21 48129895 1377831 0.02862734273573628 0.2273458229269641 chr22 51304566 1143391 0.022286339972157645 0.18504016650995467 chrMT 16571 12391 0.7477520970369923 1.129306602605351 chrX 155270560 3251152 0.020938624810781903 0.203185280248265 chrY 59373566 228880 0.0038549141548951263 0.1415815540093054