In this section

Oryza sativa Japonica Group vs Avena sativa OT3098 LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Avena sativa OT3098 (Avena sativa, Oat_OT3098_v2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 109. 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 GroupAvena sativa OT3098
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 673,155 alignment blocks

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

Uncovered: 289,069,959 out of 375,049,285
Covered: 85,979,326 out of 375,049,285

Uncovered: 3,371,674 out of 34,424,450
Matches: 24,080,188 out of 34,424,450
Mismatches: 6,089,466 out of 34,424,450
Insertions: 883,122 out of 34,424,450
Identity over aligned base-pairs: 77.5%

Avena sativa OT3098

Uncovered: 10,519,683,718 out of 10,839,200,031
Covered: 319,516,313 out of 10,839,200,031

Uncovered: 18,128,494 out of 98,289,555
Matches: 62,709,510 out of 98,289,555
Mismatches: 15,578,115 out of 98,289,555
Insertions: 1,873,436 out of 98,289,555
Identity over aligned base-pairs: 78.2%

Block size distribution

Size range All 673,155 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
5,815
31.9 kb
10 bp - 100 bp
99,232
6.3 Mb
42,692
3.0 Mb
100 bp - 1 kb
464,774
176.8 Mb
198,179
70.0 Mb
1 kb - 10 kb
103,308
178.1 Mb
81,915
203.6 Mb
10 kb - 100 kb
26
381.3 kb
3,072
60.4 Mb
100 kb - 1 Mb
64
13.4 Mb
1 Mb - 10 Mb
7
11.3 Mb