BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,274,175 number of mapped reads = 1,239,957 (97.31%) number of supplementary alignments = 10,096 (0.79%) number of secondary alignments = 0 number of mapped bases = 84,221,557 bp number of sequenced bases = 84,185,685 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 507,796 duplication rate = 36.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5181 >>>>>>> ACTG content number of A's = 24,903,240 bp (29.58%) number of C's = 17,903,707 bp (21.27%) number of T's = 23,184,530 bp (27.54%) number of G's = 18,189,319 bp (21.61%) number of N's = 4,889 bp (0.01%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 438,967 number of insertions = 10,581 mapped reads with insertion percentage = 0.84% number of deletions = 21,858 mapped reads with deletion percentage = 1.74% homopolymer indels = 40.17% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.3667X There is a 1.42% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% 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% 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 6926594 0.02778967599844014 0.46628009453318486 chr2 243199373 7358739 0.030258050870879506 0.5839951866014449 chr3 198022430 5633311 0.028447843004451568 0.2839215109466582 chr4 191154276 5569755 0.029137485786611437 0.3399413306752251 chr5 180915260 5143996 0.028433179158021276 0.29297524569361216 chr6 171115067 5019572 0.029334482860004375 0.3103971162990493 chr7 159138663 4686325 0.029448060651357865 0.33038861478861803 chr8 146364022 4342761 0.029670959711670126 0.3180670378722849 chr9 141213431 3653721 0.02587374992680406 0.30510051358079227 chr10 135534747 4000432 0.02951591446878194 0.38193739499156715 chr11 135006516 3943687 0.029211086374527285 0.32240617164152463 chr12 133851895 3889117 0.029055374972464902 0.3069412402079659 chr13 115169878 2709549 0.02352654224397112 0.25695356309297884 chr14 107349540 2583864 0.024069632715706096 0.2853454226180813 chr15 102531392 2467222 0.02406308889281441 0.261248704969546 chr16 90354753 2552630 0.028251197809151224 0.42189339366319517 chr17 81195210 2284619 0.02813736179757402 0.2976243285690013 chr18 78077248 2304790 0.0295193549854626 0.41555264572465056 chr19 59128983 1731767 0.02928795511331558 0.43903999183990566 chr20 63025520 1785771 0.028334093871815735 0.3000961234723197 chr21 48129895 1123901 0.023351411840811204 0.26736999426438923 chr22 51304566 1022020 0.01992064410017619 0.26211815128479937 chrMT 16571 114251 6.894635206082916 6.721454977884609 chrX 155270560 2600431 0.016747740202650137 0.24125570515652953 chrY 59373566 772732 0.013014748010924592 0.6163233015679531