BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089659.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 23,292,377 number of mapped reads = 19,599,384 (84.15%) number of supplementary alignments = 830 (0%) number of secondary alignments = 0 number of mapped bases = 916,471,550 bp number of sequenced bases = 916,284,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,621,635 duplication rate = 6.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9438 >>>>>>> ACTG content number of A's = 270,712,400 bp (29.54%) number of C's = 193,558,835 bp (21.12%) number of T's = 257,303,967 bp (28.08%) number of G's = 194,671,508 bp (21.25%) number of N's = 37,940 bp (0%) GC percentage = 42.37% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 4,550,675 number of insertions = 39,521 mapped reads with insertion percentage = 0.2% number of deletions = 126,405 mapped reads with deletion percentage = 0.64% homopolymer indels = 44.19% >>>>>>> Coverage mean coverageData = 0.296X std coverageData = 1.7041X There is a 16.64% of reference with a coverageData >= 1X There is a 6.15% of reference with a coverageData >= 2X There is a 2.72% of reference with a coverageData >= 3X There is a 1.37% of reference with a coverageData >= 4X There is a 0.76% of reference with a coverageData >= 5X There is a 0.46% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 76861430 0.3083700642013646 2.158705422874099 chr2 243199373 87087102 0.3580893360280168 2.84447850311539 chr3 198022430 84778891 0.4281277176529952 1.1926863085274313 chr4 191154276 41398224 0.21656969891691044 0.8108127633653995 chr5 180915260 38983994 0.2154820660236179 0.7737711606124921 chr6 171115067 57514174 0.33611402554048614 1.30369175793724 chr7 159138663 60800888 0.3820623276192788 2.978183812799467 chr8 146364022 72119203 0.4927385980142032 2.535145766026436 chr9 141213431 31944469 0.2262140985725359 1.5610099854961679 chr10 135534747 38051118 0.2807480652913308 1.5971268636197904 chr11 135006516 44669105 0.3308662894463553 1.5682871106994942 chr12 133851895 30920633 0.23100631485269596 0.8639404910665509 chr13 115169878 26079160 0.2264408059892188 0.7793802439058993 chr14 107349540 29924596 0.27875849304990036 1.048587953527026 chr15 102531392 22978413 0.2241110020236534 0.7774143579514573 chr16 90354753 18300340 0.2025387640647969 0.9126475861119021 chr17 81195210 21927074 0.2700537876557004 1.0318896538995033 chr18 78077248 43592000 0.5583188587794488 2.3907344763747975 chr19 59128983 15849415 0.2680481583794533 2.1256028085172325 chr20 63025520 20571447 0.3263986873888545 1.0355645620585276 chr21 48129895 14213879 0.2953232912725033 1.0876449063582527 chr22 51304566 7424508 0.14471437103668316 0.6086792117690096 chrMT 16571 426260 25.723251463399915 21.060334934433175 chrX 155270560 27894998 0.17965413404833472 1.2479851664585302 chrY 59373566 2160229 0.03638368293391709 0.5991805144889188