BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819025.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 = 1,526,437 number of mapped reads = 1,491,652 (97.72%) number of supplementary alignments = 23,176 (1.52%) number of secondary alignments = 0 number of mapped bases = 138,009,290 bp number of sequenced bases = 137,918,125 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 579,755 duplication rate = 31.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2589 >>>>>>> ACTG content number of A's = 40,463,761 bp (29.34%) number of C's = 28,496,402 bp (20.66%) number of T's = 38,788,949 bp (28.12%) number of G's = 30,162,337 bp (21.87%) number of N's = 6,676 bp (0%) GC percentage = 42.53% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 864,958 number of insertions = 22,128 mapped reads with insertion percentage = 1.43% number of deletions = 48,123 mapped reads with deletion percentage = 3.13% homopolymer indels = 40.56% >>>>>>> Coverage mean coverageData = 0.0446X std coverageData = 0.5512X There is a 2.38% of reference with a coverageData >= 1X There is a 0.95% of reference with a coverageData >= 2X There is a 0.48% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.13% 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 0.01% 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 13853840 0.05558196783790561 0.8857768093316419 chr2 243199373 10661136 0.04383702091205638 0.9036618146771331 chr3 198022430 8500113 0.042925000970849614 0.3493771441642121 chr4 191154276 7505046 0.03926172177283651 0.3776682140419073 chr5 180915260 7431953 0.0410797463961857 0.352429306087933 chr6 171115067 5664141 0.03310135746257809 0.35131968993839574 chr7 159138663 6759567 0.042475956958366555 0.5908209995282951 chr8 146364022 12660751 0.0865017975524067 0.5545903667297437 chr9 141213431 3594589 0.025455007888024475 0.43644347565686065 chr10 135534747 7130578 0.05261070063457602 0.6465342913831242 chr11 135006516 4674347 0.034623121449930606 0.3579960427764242 chr12 133851895 6340763 0.047371484729446675 0.37173352900895384 chr13 115169878 2922426 0.025374916173828022 0.26406050726264074 chr14 107349540 3195912 0.029771082391224033 0.30399512728196615 chr15 102531392 3558514 0.0347065804002739 0.31387983946319603 chr16 90354753 4299754 0.04758746891820954 0.674987473306014 chr17 81195210 4793312 0.05903441840965742 0.4543896118303095 chr18 78077248 3172206 0.04062907032788861 0.5640810498532212 chr19 59128983 2825756 0.04778969393063973 0.8006032082908483 chr20 63025520 3901923 0.06191020716687463 0.4515551418995095 chr21 48129895 1856099 0.038564368361908956 0.35114097789476406 chr22 51304566 1098951 0.02142014026587809 0.2651754200065007 chrMT 16571 103053 6.218876350250437 5.663966996436189 chrX 155270560 10933150 0.07041354136933621 0.4971287918921356 chrY 59373566 571410 0.009623979802729046 0.5801652841136286