Zea mays vs Oryza sativa Japonica Group LastZ results

Zea mays (Zea mays, B73_RefGen_v4) and Oryza sativa Japonica Group (Oryza sativa Japonica Group, IRGSP-1.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 85. Zea mays 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)3000
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

ParameterZea maysOryza sativa Japonica Group
Chunk size50,000,000100,100,000
Overlap0100,000
Group set size0100,100,000
Masking options{default_soft_masking => 1}{default_soft_masking => 1}

Statistics over 224,244 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Zea mays

Uncovered: 2,032,241,522 out of 2,134,373,047
Covered: 102,131,525 out of 2,134,373,047

Uncovered: 6,106,008 out of 48,311,124
Matches: 32,968,756 out of 48,311,124
Mismatches: 8,212,282 out of 48,311,124
Insertions: 1,024,078 out of 48,311,124
Identity over aligned base-pairs: 78.1%

Oryza sativa Japonica Group

Uncovered: 320,757,170 out of 374,424,240
Covered: 53,667,070 out of 374,424,240

Uncovered: 10,628,554 out of 34,124,807
Matches: 18,546,551 out of 34,124,807
Mismatches: 4,370,925 out of 34,124,807
Insertions: 578,777 out of 34,124,807
Identity over aligned base-pairs: 78.9%

Block size distribution

Size range All 224,244 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
1,137
6.8 kb
10 bp - 100 bp
29,669
2.0 Mb
13,391
984.9 kb
100 bp - 1 kb
165,742
61.6 Mb
76,029
26.2 Mb
1 kb - 10 kb
27,694
45.8 Mb
19,003
48.7 Mb
10 kb - 100 kb
2
37.4 kb
857
17.2 Mb
100 kb - 1 Mb
34
8.7 Mb
1 Mb - 10 Mb
6
7.5 Mb