Arabidopsis thaliana vs Citrus clementina LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Citrus clementina (Citrus clementina, Citrus_clementina_v1.0) 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: 131,953

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

Uncovered: 82,513,056 out of 119,667,750
Covered: 37,154,694 out of 119,667,750

Uncovered: 7,647,160 out of 33,775,569
Matches: 17,886,179 out of 33,775,569
Mismatches: 7,693,617 out of 33,775,569
Insertions: 548,613 out of 33,775,569

Citrus clementina

Uncovered: 260,001,091 out of 301,364,702
Covered: 41,363,611 out of 301,364,702

Uncovered: 6,665,809 out of 30,721,724
Matches: 16,190,513 out of 30,721,724
Mismatches: 7,160,683 out of 30,721,724
Insertions: 704,719 out of 30,721,724

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 Citrus clementina
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}