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 96. 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 size010,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 138,462 alignment blocks

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

Uncovered: 294,498,137 out of 375,049,285
Covered: 80,551,148 out of 375,049,285

Uncovered: 3,357,272 out of 34,349,962
Matches: 24,351,867 out of 34,349,962
Mismatches: 5,878,273 out of 34,349,962
Insertions: 762,550 out of 34,349,962
Identity over aligned base-pairs: 78.6%

Panicum hallii FIL2

Uncovered: 469,909,587 out of 535,889,049
Covered: 65,979,462 out of 535,889,049

Uncovered: 9,136,467 out of 38,415,885
Matches: 23,426,839 out of 38,415,885
Mismatches: 5,224,298 out of 38,415,885
Insertions: 628,281 out of 38,415,885
Identity over aligned base-pairs: 80.0%

Block size distribution

Size range All 138,462 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,230
7.0 kb
10 bp - 100 bp
18,586
1.1 Mb
6,050
414.4 kb
100 bp - 1 kb
91,993
37.6 Mb
22,342
7.5 Mb
1 kb - 10 kb
26,642
47.6 Mb
7,599
19.4 Mb
10 kb - 100 kb
11
117.7 kb
266
6.0 Mb
100 kb - 1 Mb
13
5.8 Mb
1 Mb - 10 Mb
16
47.3 Mb