Oryza sativa Japonica Group vs Panicum hallii FIL2 LastZ results

Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) and Panicum hallii FIL2 (Panicum hallii str. FIL2, PHallii_v3.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 104. 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 GroupPanicum hallii FIL2
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 189,072 alignment blocks

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

Uncovered: 294,214,372 out of 375,049,285
Covered: 80,834,913 out of 375,049,285

Uncovered: 3,400,161 out of 34,424,450
Matches: 24,325,394 out of 34,424,450
Mismatches: 5,921,175 out of 34,424,450
Insertions: 777,720 out of 34,424,450
Identity over aligned base-pairs: 78.4%

Panicum hallii FIL2

Uncovered: 454,210,703 out of 535,889,049
Covered: 81,678,346 out of 535,889,049

Uncovered: 4,842,540 out of 38,415,885
Matches: 26,551,233 out of 38,415,885
Mismatches: 6,276,249 out of 38,415,885
Insertions: 745,863 out of 38,415,885
Identity over aligned base-pairs: 79.1%

Block size distribution

Size range All 189,072 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,779
9.8 kb
10 bp - 100 bp
29,181
1.8 Mb
11,693
816.9 kb
100 bp - 1 kb
127,443
48.9 Mb
42,576
14.1 Mb
1 kb - 10 kb
30,649
54.1 Mb
12,620
30.2 Mb
10 kb - 100 kb
20
214.1 kb
302
6.6 Mb
100 kb - 1 Mb
14
6.0 Mb
1 Mb - 10 Mb
16
47.3 Mb