BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081114.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 = 3,033,894 number of mapped reads = 2,806,118 (92.49%) number of supplementary alignments = 16,443 (0.54%) number of secondary alignments = 0 number of mapped bases = 190,173,703 bp number of sequenced bases = 190,103,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 140,131 duplication rate = 4.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3671 >>>>>>> ACTG content number of A's = 52,498,379 bp (27.62%) number of C's = 37,031,260 bp (19.48%) number of T's = 58,068,586 bp (30.55%) number of G's = 42,503,340 bp (22.36%) number of N's = 2,043 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,644,724 number of insertions = 13,785 mapped reads with insertion percentage = 0.49% number of deletions = 38,801 mapped reads with deletion percentage = 1.37% homopolymer indels = 47.2% >>>>>>> Coverage mean coverageData = 0.0614X std coverageData = 0.4352X There is a 4.78% of reference with a coverageData >= 1X There is a 0.94% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 15756364 0.06321494380549608 0.5698428492765136 chr2 243199373 12849719 0.05283615184320397 0.46557520179523215 chr3 198022430 16228801 0.08195435739274587 0.3530333950217927 chr4 191154276 11098035 0.05805800023013872 0.3255180806876952 chr5 180915260 10536908 0.058242228986101006 0.29590943209494824 chr6 171115067 15592068 0.09112036872825466 0.534644251071238 chr7 159138663 9342403 0.0587060543546228 0.52278046814451 chr8 146364022 15012269 0.10256802727107349 0.4936430305406962 chr9 141213431 9282845 0.06573627546801833 0.5344811438406177 chr10 135534747 8899293 0.06566060141020516 0.3994969057501443 chr11 135006516 8706378 0.0644885762402757 0.4120448829845563 chr12 133851895 8462994 0.06322655349780441 0.32967850751821864 chr13 115169878 4555764 0.03955690566937997 0.2439765618313859 chr14 107349540 5437077 0.050648349308250414 0.3600330579484631 chr15 102531392 5075599 0.049502878103907924 0.277601622894738 chr16 90354753 4859236 0.05377952834423663 0.35431106399894374 chr17 81195210 4510477 0.05555102326849084 0.30507644525442706 chr18 78077248 4429628 0.05673391562161617 0.8734101293176869 chr19 59128983 4722480 0.07986743150985702 0.5152242664600165 chr20 63025520 3242339 0.051444859161812545 0.30340465669737227 chr21 48129895 3353820 0.06968267850989494 0.4248844048406459 chr22 51304566 1941792 0.037848327183978125 0.23784009586913143 chrMT 16571 351267 21.197694767968137 13.214964486600216 chrX 155270560 5465247 0.035198217872080835 0.26423238133530563 chrY 59373566 460900 0.007762713797584602 0.18976736331198174