Oryza sativa Japonica Group vs Triticum urartu LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Triticum urartu (Triticum urartu, ASM34745v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 73. Oryza sativa Japonica Group 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

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)
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterOryza sativa Japonica GroupTriticum urartu
Chunk size50,000,000100,100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 143,410 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Oryza sativa Japonica Group

Uncovered: 304,512,397 out of 374,424,240
Covered: 69,911,843 out of 374,424,240

Uncovered: 6,129,279 out of 34,124,807
Matches: 21,500,232 out of 34,124,807
Mismatches: 5,740,876 out of 34,124,807
Insertions: 754,420 out of 34,124,807
Identity over aligned base-pairs: 76.8%

Triticum urartu

Uncovered: 3,693,701,355 out of 3,747,163,292
Covered: 53,461,937 out of 3,747,163,292

Uncovered: 15,341,134 out of 36,143,424
Matches: 16,518,982 out of 36,143,424
Mismatches: 3,891,307 out of 36,143,424
Insertions: 392,001 out of 36,143,424
Identity over aligned base-pairs: 79.4%