BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082770.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 5,208,336 number of mapped reads = 4,661,905 (89.51%) number of supplementary alignments = 38,208 (0.73%) number of secondary alignments = 0 number of mapped bases = 320,473,549 bp number of sequenced bases = 320,354,413 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 244,469 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.297 >>>>>>> ACTG content number of A's = 92,260,640 bp (28.8%) number of C's = 60,013,371 bp (18.73%) number of T's = 101,718,092 bp (31.75%) number of G's = 66,345,114 bp (20.71%) number of N's = 17,196 bp (0.01%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 2,830,947 number of insertions = 25,065 mapped reads with insertion percentage = 0.53% number of deletions = 69,660 mapped reads with deletion percentage = 1.48% homopolymer indels = 47.59% >>>>>>> Coverage mean coverageData = 0.1035X std coverageData = 0.7549X There is a 7.43% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 29694534 0.11913524580546582 1.464939217970974 chr2 243199373 33227421 0.1366262609566843 0.937477347169725 chr3 198022430 23972963 0.12106185647757176 0.4527400421098672 chr4 191154276 18965527 0.09921581351389702 0.42984878148325445 chr5 180915260 16997176 0.09395103541846056 0.40309012733820543 chr6 171115067 22870146 0.13365360748741079 0.7852189357209959 chr7 159138663 16636290 0.10453958633547147 0.633749114344765 chr8 146364022 23516700 0.16067268225247322 1.027001655947081 chr9 141213431 9570198 0.06777115981269516 0.6871241552834446 chr10 135534747 11585317 0.08547857473036047 0.5260595541434869 chr11 135006516 12979993 0.09614345577216436 0.6405692962963428 chr12 133851895 10241854 0.07651631678430851 0.37213271036342643 chr13 115169878 6614373 0.057431449219734344 0.30927019466341726 chr14 107349540 6929868 0.06455424028831423 0.4042454310151861 chr15 102531392 6254217 0.0609980697423868 0.3157998388990158 chr16 90354753 12253126 0.13561130536209867 0.5476580175571335 chr17 81195210 7702401 0.09486275114012267 0.4846641690250821 chr18 78077248 14636473 0.18746143562846887 1.535891547978397 chr19 59128983 5242013 0.08865386708917351 0.9289071443983453 chr20 63025520 6619809 0.10503378631386143 0.4449942736175894 chr21 48129895 6626922 0.1376882704605942 0.5075672086786454 chr22 51304566 4045605 0.07885467737900756 0.3610652376068754 chrMT 16571 494384 29.834288817814254 18.256306785871075 chrX 155270560 12281620 0.07909818834942052 0.4481890587085854 chrY 59373566 514619 0.008667476701668888 0.17225351505610156