Arabidopsis thaliana vs Glycine max LastZ Results

Back to all analyses

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Glycine max (Glycine max, V1.0) 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: 265,600

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

Uncovered: 82,769,153 out of 119,667,750
Covered: 36,898,597 out of 119,667,750

Uncovered: 8,374,790 out of 33,775,569
Matches: 17,062,528 out of 33,775,569
Mismatches: 7,704,822 out of 33,775,569
Insertions: 633,429 out of 33,775,569

Glycine max

Uncovered: 893,049,188 out of 973,344,380
Covered: 80,295,192 out of 973,344,380

Uncovered: 16,241,120 out of 64,476,920
Matches: 32,510,890 out of 64,476,920
Mismatches: 14,476,443 out of 64,476,920
Insertions: 1,248,467 out of 64,476,920

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}