Oryza meridionalis vs Oryza glumaepatula LastZ Results

Back to all analyses

Oryza meridionalis (Oryza meridionalis, Oryza_meridionalis_v1.3) and Oryza glumaepatula (Oryza glumaepatula, ALNU02000000) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 79. Oryza meridionalis was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 226,227

Genome coverage (bp) Coding exon coverage (bp)
Oryza meridionalis

Uncovered: 131,746,191 out of 335,668,232
Covered: 203,922,041 out of 335,668,232

Uncovered: 683,469 out of 35,224,824
Matches: 33,179,701 out of 35,224,824
Mismatches: 1,095,854 out of 35,224,824
Insertions: 265,800 out of 35,224,824

Oryza glumaepatula

Uncovered: 188,686,562 out of 372,860,283
Covered: 184,173,721 out of 372,860,283

Uncovered: 7,238,958 out of 41,246,944
Matches: 32,933,263 out of 41,246,944
Mismatches: 838,076 out of 41,246,944
Insertions: 236,647 out of 41,246,944

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza meridionalis Oryza glumaepatula
Chunk size 30,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1}