Arabidopsis thaliana vs Solanum tuberosum LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Solanum tuberosum (Solanum tuberosum, SolTub_3.0) 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: 153,848

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

Uncovered: 85,513,927 out of 119,667,750
Covered: 34,153,823 out of 119,667,750

Uncovered: 9,465,582 out of 33,775,569
Matches: 16,047,342 out of 33,775,569
Mismatches: 7,720,356 out of 33,775,569
Insertions: 542,289 out of 33,775,569

Solanum tuberosum

Uncovered: 767,951,720 out of 810,654,046
Covered: 42,702,326 out of 810,654,046

Uncovered: 15,245,210 out of 36,745,425
Matches: 14,282,098 out of 36,745,425
Mismatches: 6,651,675 out of 36,745,425
Insertions: 566,442 out of 36,745,425

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 Solanum tuberosum
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}