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Arabidopsis thaliana vs Triticum dicoccoides LastZ Results

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Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Triticum dicoccoides (Triticum dicoccoides, WEWSeq_v.1.0) 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: 359,368

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

Uncovered: 91,559,711 out of 119,667,750
Covered: 28,108,039 out of 119,667,750

Uncovered: 13,622,876 out of 33,775,569
Matches: 12,879,126 out of 33,775,569
Mismatches: 6,825,785 out of 33,775,569
Insertions: 447,782 out of 33,775,569

Triticum dicoccoides

Uncovered: 9,963,479,210 out of 10,079,039,394
Covered: 115,560,184 out of 10,079,039,394

Uncovered: 54,144,821 out of 100,651,268
Matches: 29,626,179 out of 100,651,268
Mismatches: 15,675,218 out of 100,651,268
Insertions: 1,205,050 out of 100,651,268

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 dicoccoides
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}