Arabidopsis thaliana vs Glycine max LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, Glycine_max_v2.1) 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: 263,764

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

Uncovered: 82,627,830 out of 119,667,750
Covered: 37,039,920 out of 119,667,750

Uncovered: 8,416,254 out of 33,775,569
Matches: 16,949,212 out of 33,775,569
Mismatches: 7,779,771 out of 33,775,569
Insertions: 630,332 out of 33,775,569

Glycine max

Uncovered: 898,147,705 out of 978,491,270
Covered: 80,343,565 out of 978,491,270

Uncovered: 17,405,539 out of 65,618,132
Matches: 32,445,446 out of 65,618,132
Mismatches: 14,505,912 out of 65,618,132
Insertions: 1,261,235 out of 65,618,132

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}