Ensembl Genomes HomeEnsembl Plants HomeEnsembl Plants Home ▼
More ▼
Search »

Oryza sativa Japonica Group vs Oryza sativa Japonica Group LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Oryza sativa Japonica Group was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
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

Chunking parameters

ParameterOryza sativa Japonica Group (reference)Oryza sativa Japonica Group (non-reference)
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 1,354,149 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 13,961,074,617 out of 14,547,261,565
Covered: 586,186,948 out of 14,547,261,565

Uncovered: 12,047,551 out of 136,655,258
Matches: 96,121,876 out of 136,655,258
Mismatches: 25,678,140 out of 136,655,258
Insertions: 2,807,691 out of 136,655,258
Identity over aligned base-pairs: 77.1%