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mummer4 / mummer

Mummer alignment tool
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How should I understande the "AlignedBases" from the dnadiff.report file #173

Open fsq9451 opened 3 years ago

fsq9451 commented 3 years ago

Dear officer,

I have aligned two homologous chromosome with high heterogeneity using nucmer, delta-filter and dnadiff, get the report file with the information: [Bases] TotalBases 22071000 22382214 AlignedBases 12953069(58.6882%) 12986449(58.0213%) UnalignedBases 9117931(41.3118%) 9395765(41.9787%)

(1) How should I understand the aligned bases? (2) when I calculated the snp percentage, should I calibrate the snp rate by the aligned bases rates?

Thank you very much! Shiqian