Arabidopsis thaliana vs Triticum urartu LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum urartu (Triticum urartu, ASM34745v1) 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: 136,892

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

Uncovered: 93,686,702 out of 119,667,750
Covered: 25,981,048 out of 119,667,750

Uncovered: 15,349,787 out of 33,775,569
Matches: 11,422,270 out of 33,775,569
Mismatches: 6,642,613 out of 33,775,569
Insertions: 360,899 out of 33,775,569

Triticum urartu

Uncovered: 3,710,985,707 out of 3,747,163,292
Covered: 36,177,585 out of 3,747,163,292

Uncovered: 18,605,657 out of 36,194,921
Matches: 11,290,792 out of 36,194,921
Mismatches: 5,899,582 out of 36,194,921
Insertions: 398,890 out of 36,194,921

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 Triticum urartu
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}