BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472577.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 5,933,710 number of mapped reads = 5,359,831 (90.33%) number of supplementary alignments = 187,032 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,707,042 number of mapped paired reads (second in pair) = 2,652,789 number of mapped paired reads (both in pair) = 5,208,694 number of mapped paired reads (singletons) = 151,137 number of mapped bases = 431,295,900 bp number of sequenced bases = 431,115,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 740,961 duplication rate = 12.14% >>>>>>> Insert size mean insert size = 277,562.4102 std insert size = 5,089,807.6144 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 50.3556 >>>>>>> ACTG content number of A's = 111,374,765 bp (25.83%) number of C's = 84,924,427 bp (19.7%) number of T's = 129,967,984 bp (30.15%) number of G's = 104,563,139 bp (24.25%) number of N's = 284,723 bp (0.07%) GC percentage = 43.95% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 5,258,011 number of insertions = 41,553 mapped reads with insertion percentage = 0.76% number of deletions = 96,958 mapped reads with deletion percentage = 1.77% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.1393X std coverageData = 1.4189X There is a 8.62% of reference with a coverageData >= 1X There is a 3.34% of reference with a coverageData >= 2X There is a 0.91% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 27821251 0.11161958549342993 1.6113528729174065 chr2 243199373 43270911 0.1779236124922082 1.874015061298239 chr3 198022430 22924253 0.11576594126231053 0.46858114427360975 chr4 191154276 22383496 0.11709649644457862 0.7693553486962459 chr5 180915260 20784693 0.11488634513196952 0.49562436852634467 chr6 171115067 28861692 0.1686683265594607 0.8257899130469244 chr7 159138663 36382630 0.22862219220730792 2.4664439049408435 chr8 146364022 21462276 0.14663628196825584 1.3101861888982245 chr9 141213431 14956822 0.10591642660392551 1.4410145679823514 chr10 135534747 16438948 0.1212895465101654 1.2542006971051627 chr11 135006516 15929372 0.11798965318088796 1.0739905479466212 chr12 133851895 22289162 0.16652107913750494 0.5887319123048526 chr13 115169878 20767290 0.18031876355725582 0.611483472903005 chr14 107349540 11072030 0.10313998550902034 3.7772277578361404 chr15 102531392 9963383 0.09717397575173856 0.43560466126291164 chr16 90354753 15276189 0.1690690140008462 0.7702634400843379 chr17 81195210 16162040 0.19905164356370283 1.1118859559193162 chr18 78077248 9771404 0.1251504663688966 2.477259833915098 chr19 59128983 8604019 0.14551271751114 1.1445430960097067 chr20 63025520 14595920 0.23158745854060386 0.9111636250288382 chr21 48129895 6537375 0.13582774281971735 0.6435573486002721 chr22 51304566 4566219 0.089002195243207 0.4245360038369439 chrMT 16571 12773 0.7708044173556212 1.2190316894275817 chrX 155270560 19504173 0.12561410868873019 0.6831715154961587 chrY 59373566 957579 0.01612803583332017 0.6044362359309933