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Arabidopsis thaliana vs Oryza longistaminata LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Oryza longistaminata (Oryza longistaminata, O_longistaminata_v1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)3000
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

Chunking parameters

ParameterArabidopsis thalianaOryza longistaminata
Chunk size30,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}

Statistics over 80,763 alignment blocks

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

Uncovered: 93,513,658 out of 119,667,750
Covered: 26,154,092 out of 119,667,750

Uncovered: 13,993,484 out of 33,462,323
Matches: 12,727,695 out of 33,462,323
Mismatches: 6,377,717 out of 33,462,323
Insertions: 363,427 out of 33,462,323
Identity over aligned base-pairs: 65.4%

Oryza longistaminata

Uncovered: 308,172,523 out of 326,442,508
Covered: 18,269,985 out of 326,442,508

Uncovered: 22,749,820 out of 34,512,301
Matches: 7,660,379 out of 34,512,301
Mismatches: 3,826,340 out of 34,512,301
Insertions: 275,762 out of 34,512,301
Identity over aligned base-pairs: 65.1%