Oryza sativa Japonica Group vs Arabidopsis halleri LastZ Results

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Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Oryza sativa Japonica Group 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: 122,843

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

Uncovered: 344,856,627 out of 375,049,285
Covered: 30,192,658 out of 375,049,285

Uncovered: 15,792,351 out of 34,403,043
Matches: 11,868,412 out of 34,403,043
Mismatches: 6,278,757 out of 34,403,043
Insertions: 463,523 out of 34,403,043

Arabidopsis halleri subsp. gemmifera

Uncovered: 167,241,843 out of 196,243,198
Covered: 29,001,355 out of 196,243,198

Uncovered: 18,384,834 out of 38,698,211
Matches: 13,188,664 out of 38,698,211
Mismatches: 6,724,393 out of 38,698,211
Insertions: 400,320 out of 38,698,211

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
Other parameters (other)--ambiguous=iupac

Chunking parameters

Oryza sativa Japonica Group Arabidopsis halleri
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}