BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524601.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 = 991,427 number of mapped reads = 920,859 (92.88%) number of supplementary alignments = 1,944 (0.2%) number of secondary alignments = 0 number of mapped bases = 53,460,951 bp number of sequenced bases = 53,444,939 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,525 duplication rate = 2.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2196 >>>>>>> ACTG content number of A's = 13,190,973 bp (24.68%) number of C's = 9,828,103 bp (18.39%) number of T's = 17,283,875 bp (32.34%) number of G's = 13,141,638 bp (24.59%) number of N's = 350 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 247,575 number of insertions = 2,912 mapped reads with insertion percentage = 0.32% number of deletions = 9,375 mapped reads with deletion percentage = 1.01% homopolymer indels = 43.87% >>>>>>> Coverage mean coverageData = 0.0173X std coverageData = 0.1785X There is a 1.58% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5255322 0.02108448909340932 0.2833727776074533 chr2 243199373 4101890 0.016866367496761597 0.19766090326301725 chr3 198022430 3362973 0.01698278826292557 0.13936798460085612 chr4 191154276 2432765 0.012726709812131014 0.13563072244405835 chr5 180915260 3399324 0.018789592431285234 0.1467528283844905 chr6 171115067 3571155 0.020869903875852146 0.16260415762724958 chr7 159138663 3307989 0.020786834183720647 0.23138561180138903 chr8 146364022 4721924 0.032261507544524844 0.2294212929762586 chr9 141213431 1964797 0.013913669444091335 0.16584830631713857 chr10 135534747 2311742 0.017056452689582252 0.1811068243846968 chr11 135006516 3374137 0.02499240110751395 0.19251111778819735 chr12 133851895 1787214 0.013352175551941197 0.12696790571441385 chr13 115169878 1336429 0.011603980339373113 0.11797245373512102 chr14 107349540 979435 0.009123793171354064 0.10519995823046653 chr15 102531392 1329959 0.012971237140718815 0.1258569603063633 chr16 90354753 1566076 0.017332524831316844 0.14781245431849657 chr17 81195210 1158045 0.014262479276794776 0.12918086987787603 chr18 78077248 1462304 0.018728938806859587 0.2355554757213997 chr19 59128983 1057970 0.01789257900816593 0.2148262433124098 chr20 63025520 1012014 0.016057209841346808 0.13855056951996764 chr21 48129895 478562 0.009943134095763143 0.11577409480780278 chr22 51304566 909503 0.01772752546040444 0.14289725834888312 chrMT 16571 3767 0.22732484460805022 0.5056358081427996 chrX 155270560 2442073 0.01572785594384409 0.1489396063648763 chrY 59373566 133582 0.0022498564428486576 0.07412475847311344