Arabidopsis thaliana vs Oryza barthii LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza barthii (Oryza barthii, O.barthii_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release . Arabidopsis thaliana 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: 110,934

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,878,831 out of 119,667,750
Covered: 25,788,919 out of 119,667,750

Uncovered: 14,744,635 out of 33,775,569
Matches: 12,346,021 out of 33,775,569
Mismatches: 6,307,169 out of 33,775,569
Insertions: 377,744 out of 33,775,569

Oryza barthii

Uncovered: 280,400,139 out of 308,272,304
Covered: 27,872,165 out of 308,272,304

Uncovered: 20,267,981 out of 39,538,509
Matches: 12,427,083 out of 39,538,509
Mismatches: 6,390,299 out of 39,538,509
Insertions: 453,146 out of 39,538,509

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

Arabidopsis thaliana Oryza barthii
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}