Zea mays vs Setaria italica LastZ results

Zea mays (Zea mays, B73_RefGen_v4) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. 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 maysSetaria italica
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 367,182 alignment blocks

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

Uncovered: 2,018,470,650 out of 2,135,083,061
Covered: 116,612,411 out of 2,135,083,061

Uncovered: 14,422,182 out of 48,442,923
Matches: 28,933,198 out of 48,442,923
Mismatches: 4,438,145 out of 48,442,923
Insertions: 649,398 out of 48,442,923
Identity over aligned base-pairs: 85.0%

Setaria italica

Uncovered: 293,108,768 out of 405,732,883
Covered: 112,624,115 out of 405,732,883

Uncovered: 5,946,301 out of 39,583,990
Matches: 27,524,063 out of 39,583,990
Mismatches: 5,401,424 out of 39,583,990
Insertions: 712,202 out of 39,583,990
Identity over aligned base-pairs: 81.8%

Block size distribution

Size range All 367,182 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
3,273
20.0 kb
10 bp - 100 bp
62,868
4.0 Mb
28,877
2.0 Mb
100 bp - 1 kb
258,073
89.6 Mb
136,616
44.5 Mb
1 kb - 10 kb
42,960
75.7 Mb
24,327
57.5 Mb
10 kb - 100 kb
8
113.9 kb
911
20.0 Mb
100 kb - 1 Mb
53
13.0 Mb
1 Mb - 10 Mb
13
32.3 Mb