BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068091.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 = 4,471,626 number of mapped reads = 3,759,810 (84.08%) number of supplementary alignments = 23,082 (0.52%) number of secondary alignments = 0 number of mapped bases = 236,153,239 bp number of sequenced bases = 236,012,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,420,930 duplication rate = 20.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9728 >>>>>>> ACTG content number of A's = 58,912,292 bp (24.96%) number of C's = 42,889,235 bp (18.17%) number of T's = 76,669,041 bp (32.49%) number of G's = 57,516,879 bp (24.37%) number of N's = 25,316 bp (0.01%) GC percentage = 42.54% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,518,309 number of insertions = 14,646 mapped reads with insertion percentage = 0.39% number of deletions = 78,256 mapped reads with deletion percentage = 2.05% homopolymer indels = 45.06% >>>>>>> Coverage mean coverageData = 0.0763X std coverageData = 0.9925X There is a 1.95% of reference with a coverageData >= 1X There is a 1.22% of reference with a coverageData >= 2X There is a 0.93% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.27% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% 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 21177082 0.08496300596980258 1.6444685293100312 chr2 243199373 23222124 0.09548595341156574 1.3028054228164077 chr3 198022430 15006330 0.0757809607729791 0.7806537771427347 chr4 191154276 11227046 0.0587329053523239 0.682084181111411 chr5 180915260 12515141 0.06917681239271911 0.7333192815648255 chr6 171115067 17033013 0.09954128118945832 0.9720486427817837 chr7 159138663 20903872 0.13135633796294996 1.374174172981111 chr8 146364022 9942992 0.0679333067247906 1.0221490877867923 chr9 141213431 7859843 0.05565931614536014 0.7342570069212085 chr10 135534747 12247243 0.09036238507900855 0.9413075630522826 chr11 135006516 11362055 0.08415930828109067 0.8845510005078747 chr12 133851895 9330703 0.06970915876835364 0.7595242730568016 chr13 115169878 5320631 0.046198112669703445 0.5973686513682696 chr14 107349540 4563749 0.04251298142497863 0.5793603163989924 chr15 102531392 4719969 0.046034379402554094 0.6205669881441043 chr16 90354753 5613167 0.062123649433251174 0.721224022137491 chr17 81195210 6973116 0.08588087893362183 0.8635876549109869 chr18 78077248 6071233 0.0777593108814491 1.1986890542453632 chr19 59128983 5354281 0.09055256370636376 1.291041822004969 chr20 63025520 3600991 0.057135442912648715 0.6870143152312164 chr21 48129895 3620227 0.07521784537448087 0.792905944020369 chr22 51304566 2689073 0.05241391185338163 0.6397926054982069 chrMT 16571 344818 20.808520910023535 18.20319914740099 chrX 155270560 14730613 0.09487061166005971 0.8897449715224868 chrY 59373566 723927 0.01219274921098726 0.37530326570541467