Arabidopsis thaliana vs Glycine max LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, Glycine_max_v2.0) 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: 263,333

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

Uncovered: 82,669,201 out of 119,667,750
Covered: 36,998,549 out of 119,667,750

Uncovered: 8,427,625 out of 33,775,569
Matches: 16,944,589 out of 33,775,569
Mismatches: 7,774,586 out of 33,775,569
Insertions: 628,769 out of 33,775,569

Glycine max

Uncovered: 898,339,146 out of 978,416,860
Covered: 80,077,714 out of 978,416,860

Uncovered: 17,495,021 out of 65,631,894
Matches: 32,406,471 out of 65,631,894
Mismatches: 14,473,316 out of 65,631,894
Insertions: 1,257,086 out of 65,631,894

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 Glycine max
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}