Arabidopsis thaliana vs Olea europaea var. sylvestris LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Olea europaea var. sylvestris (Olea europaea var. sylvestris, O_europaea_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: 210,672

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

Uncovered: 81,212,045 out of 119,667,750
Covered: 38,455,705 out of 119,667,750

Uncovered: 8,980,949 out of 33,775,569
Matches: 15,519,812 out of 33,775,569
Mismatches: 8,724,131 out of 33,775,569
Insertions: 550,677 out of 33,775,569

Olea europaea var. sylvestris

Uncovered: 1,076,944,662 out of 1,140,989,389
Covered: 64,044,727 out of 1,140,989,389

Uncovered: 22,364,326 out of 52,755,300
Matches: 20,318,634 out of 52,755,300
Mismatches: 9,295,019 out of 52,755,300
Insertions: 777,321 out of 52,755,300

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 Olea europaea var. sylvestris
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options