Zea mays vs Arabidopsis thaliana LastZ results

Zea mays (Zea mays, B73_RefGen_v4) and Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) 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 maysArabidopsis thaliana
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 139,180 alignment blocks

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

Uncovered: 2,091,499,146 out of 2,134,373,047
Covered: 42,873,901 out of 2,134,373,047

Uncovered: 21,906,852 out of 48,311,124
Matches: 17,122,958 out of 48,311,124
Mismatches: 8,629,592 out of 48,311,124
Insertions: 651,722 out of 48,311,124
Identity over aligned base-pairs: 64.8%

Arabidopsis thaliana

Uncovered: 100,397,387 out of 119,667,750
Covered: 19,270,363 out of 119,667,750

Uncovered: 19,299,348 out of 33,462,323
Matches: 9,200,308 out of 33,462,323
Mismatches: 4,664,880 out of 33,462,323
Insertions: 297,787 out of 33,462,323
Identity over aligned base-pairs: 65.0%

Block size distribution

Size range All 139,180 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
774
4.1 kb
10 bp - 100 bp
22,606
1.6 Mb
6,542
491.3 kb
100 bp - 1 kb
109,542
34.1 Mb
45,072
16.5 Mb
1 kb - 10 kb
6,258
9.1 Mb
14,104
27.4 Mb
10 kb - 100 kb
28
432.1 kb