Arabidopsis thaliana vs Capsicum annuum LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Capsicum annuum (Capsicum annuum, ASM51225v2) 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: 197,496

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

Uncovered: 86,333,345 out of 119,667,750
Covered: 33,334,405 out of 119,667,750

Uncovered: 9,625,824 out of 33,775,569
Matches: 16,026,272 out of 33,775,569
Mismatches: 7,585,171 out of 33,775,569
Insertions: 538,302 out of 33,775,569

Capsicum annuum

Uncovered: 3,010,943,505 out of 3,063,864,880
Covered: 52,921,375 out of 3,063,864,880

Uncovered: 14,072,818 out of 39,113,865
Matches: 16,708,122 out of 39,113,865
Mismatches: 7,730,009 out of 39,113,865
Insertions: 602,916 out of 39,113,865

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 Capsicum annuum
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}