Hordeum vulgare vs Oryza sativa Japonica LastZ Results

Back to all analyses

Hordeum vulgare (Hordeum vulgare, ASM32608v1) and Oryza sativa Japonica (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 80. Hordeum vulgare 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: 273,027

Genome coverage (bp) Coding exon coverage (bp)
Hordeum vulgare

Uncovered: 3,937,642,356 out of 4,045,300,851
Covered: 107,658,495 out of 4,045,300,851

Uncovered: 2,153,862 out of 27,753,036
Matches: 20,145,947 out of 27,753,036
Mismatches: 4,922,742 out of 27,753,036
Insertions: 530,485 out of 27,753,036

Oryza sativa Japonica Group

Uncovered: 300,817,720 out of 374,424,240
Covered: 73,606,520 out of 374,424,240

Uncovered: 4,215,443 out of 34,124,807
Matches: 23,189,271 out of 34,124,807
Mismatches: 5,920,229 out of 34,124,807
Insertions: 799,864 out of 34,124,807

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

Hordeum vulgare Oryza sativa Japonica
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}