Arabidopsis thaliana vs Ostreococcus lucimarinus LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Ostreococcus lucimarinus (Ostreococcus lucimarinus CCE9901, ASM9206v1) 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: 11,176

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

Uncovered: 117,450,957 out of 119,667,750
Covered: 2,216,793 out of 119,667,750

Uncovered: 31,705,252 out of 33,775,569
Matches: 1,290,726 out of 33,775,569
Mismatches: 733,466 out of 33,775,569
Insertions: 46,125 out of 33,775,569

Ostreococcus lucimarinus CCE9901

Uncovered: 11,936,367 out of 13,204,888
Covered: 1,268,521 out of 13,204,888

Uncovered: 7,997,677 out of 9,226,744
Matches: 764,452 out of 9,226,744
Mismatches: 443,286 out of 9,226,744
Insertions: 21,329 out of 9,226,744

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 Ostreococcus lucimarinus
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}