BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080651.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,256,263 number of mapped reads = 1,139,288 (90.69%) number of supplementary alignments = 9,186 (0.73%) number of secondary alignments = 0 number of mapped bases = 75,618,263 bp number of sequenced bases = 75,589,749 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,284 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3562 >>>>>>> ACTG content number of A's = 20,269,236 bp (26.81%) number of C's = 14,168,233 bp (18.74%) number of T's = 23,656,580 bp (31.3%) number of G's = 17,492,437 bp (23.14%) number of N's = 3,263 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 511,137 number of insertions = 5,608 mapped reads with insertion percentage = 0.49% number of deletions = 17,582 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.72% >>>>>>> Coverage mean coverageData = 0.0244X std coverageData = 0.2074X There is a 2.16% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 9267060 0.03717968670577555 0.24824806918585823 chr2 243199373 5124936 0.021072981960360563 0.31349028808959045 chr3 198022430 4657013 0.02351760353612467 0.16881073132672594 chr4 191154276 3218082 0.016834998762988697 0.144817651243258 chr5 180915260 3388552 0.018730050743093755 0.15021454102208437 chr6 171115067 4629674 0.027055910862601014 0.2124391990474278 chr7 159138663 4736314 0.029762182933508748 0.33102417804937473 chr8 146364022 8855027 0.06050002506763581 0.2923782304455696 chr9 141213431 2407246 0.017046862914902195 0.15884944043999968 chr10 135534747 3590686 0.026492733999791213 0.18580764730239926 chr11 135006516 3141032 0.02326578074201989 0.1749211639132289 chr12 133851895 2485847 0.018571623509700777 0.14994012792380265 chr13 115169878 1570926 0.013640076965263434 0.1284185862307252 chr14 107349540 1504456 0.014014554696741132 0.13217186102717393 chr15 102531392 1419899 0.013848431902689862 0.13501472297506886 chr16 90354753 1969862 0.021801420894814464 0.1654788319198009 chr17 81195210 1286438 0.01584376713848021 0.13986988044191345 chr18 78077248 2326707 0.029800064162097517 0.22872332775127638 chr19 59128983 1255669 0.021236100069571634 0.1783187273956869 chr20 63025520 2013269 0.03194371105545817 0.19916754792105412 chr21 48129895 1049937 0.021814653865336712 0.16448289661725546 chr22 51304566 829353 0.016165286341180626 0.14000079248867123 chrMT 16571 5024 0.3031802546617585 0.6337148384284134 chrX 155270560 4745364 0.030561904330093224 0.19858076024640603 chrY 59373566 139890 0.002356099008774376 0.05418284052075426