BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716355.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 = 429,653 number of mapped reads = 354,581 (82.53%) number of supplementary alignments = 1,232 (0.29%) number of secondary alignments = 0 number of mapped bases = 20,535,721 bp number of sequenced bases = 20,528,838 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,865 duplication rate = 1.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4468 >>>>>>> ACTG content number of A's = 5,233,084 bp (25.49%) number of C's = 3,632,668 bp (17.7%) number of T's = 6,465,815 bp (31.5%) number of G's = 5,196,915 bp (25.32%) number of N's = 356 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 108,833 number of insertions = 1,399 mapped reads with insertion percentage = 0.39% number of deletions = 4,223 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.85% >>>>>>> Coverage mean coverageData = 0.0066X std coverageData = 0.0959X There is a 0.64% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1732067 0.0069490980325381015 0.12155360361569043 chr2 243199373 1672005 0.006875038283918602 0.11979513844018273 chr3 198022430 1174565 0.005931474530435769 0.07888256421983666 chr4 191154276 1255416 0.006567553843263229 0.08908829206201893 chr5 180915260 1167389 0.006452683980334218 0.08234314355478169 chr6 171115067 1095863 0.006404246097159872 0.0856580199104094 chr7 159138663 1204850 0.007571070268448843 0.10912927046061979 chr8 146364022 1091758 0.007459196495707122 0.11957268041487533 chr9 141213431 669164 0.004738671068759742 0.07491661368753993 chr10 135534747 923308 0.006812334256985775 0.10278812140775449 chr11 135006516 719447 0.005328979824944153 0.07999146174310158 chr12 133851895 1032837 0.0077162672967760375 0.08995445547932612 chr13 115169878 617368 0.005360498862384833 0.07489731222092859 chr14 107349540 673847 0.0062771298321352845 0.08149099946372426 chr15 102531392 745409 0.007270056374539419 0.08698985800824968 chr16 90354753 690263 0.0076394763649013575 0.09093117327889191 chr17 81195210 863814 0.010638731028591464 0.1064997908649187 chr18 78077248 382451 0.004898366807190745 0.09443612231109755 chr19 59128983 513093 0.008677521140520885 0.10982344754493689 chr20 63025520 685809 0.01088144929228668 0.10800498573315377 chr21 48129895 267828 0.005564691134273199 0.08221009726259428 chr22 51304566 195174 0.0038042228054321714 0.06309771147112855 chrMT 16571 3349 0.20210005431174943 0.47799738376922835 chrX 155270560 1066065 0.006865854029250619 0.08629304272565086 chrY 59373566 92582 0.00155931344935556 0.0690332170782849