Oryza sativa Japonica Group vs Hordeum vulgare LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Hordeum vulgare (Hordeum vulgare subsp. vulgare, IBSC_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 90. 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

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

Chunking parameters

ParameterOryza sativa Japonica GroupHordeum vulgare
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 310,667 alignment blocks

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

Uncovered: 299,111,836 out of 374,424,240
Covered: 75,312,404 out of 374,424,240

Uncovered: 3,850,883 out of 34,124,807
Matches: 23,388,216 out of 34,124,807
Mismatches: 6,051,107 out of 34,124,807
Insertions: 834,601 out of 34,124,807
Identity over aligned base-pairs: 77.3%

Hordeum vulgare

Uncovered: 4,713,893,515 out of 4,833,907,081
Covered: 120,013,566 out of 4,833,907,081

Uncovered: 6,138,522 out of 44,392,268
Matches: 29,622,451 out of 44,392,268
Mismatches: 7,639,758 out of 44,392,268
Insertions: 991,537 out of 44,392,268
Identity over aligned base-pairs: 77.4%

Block size distribution

Size range All 310,667 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,938
11.1 kb
10 bp - 100 bp
46,408
3.0 Mb
23,698
1.7 Mb
100 bp - 1 kb
224,522
82.0 Mb
112,326
39.7 Mb
1 kb - 10 kb
37,781
64.0 Mb
37,829
95.6 Mb
10 kb - 100 kb
18
225.3 kb
816
12.3 Mb