Arabidopsis thaliana vs Arabidopsis halleri LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Arabidopsis halleri (Arabidopsis halleri subsp. gemmifera, Ahal2.2) 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: 193,242

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

Uncovered: 22,641,739 out of 119,667,750
Covered: 97,026,011 out of 119,667,750

Uncovered: 604,788 out of 33,775,569
Matches: 29,809,064 out of 33,775,569
Mismatches: 3,143,002 out of 33,775,569
Insertions: 218,715 out of 33,775,569

Arabidopsis halleri subsp. gemmifera

Uncovered: 73,574,711 out of 196,243,198
Covered: 122,668,487 out of 196,243,198

Uncovered: 3,461,504 out of 38,698,211
Matches: 32,236,909 out of 38,698,211
Mismatches: 2,688,048 out of 38,698,211
Insertions: 311,750 out of 38,698,211

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 Arabidopsis halleri
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}