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Arabidopsis thaliana vs Setaria italica LastZ results

Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 93. Arabidopsis thaliana 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

ParameterArabidopsis thalianaSetaria 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 118,568 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Arabidopsis thaliana

Uncovered: 93,296,869 out of 119,667,750
Covered: 26,370,881 out of 119,667,750

Uncovered: 14,199,221 out of 33,775,569
Matches: 12,679,009 out of 33,775,569
Mismatches: 6,498,834 out of 33,775,569
Insertions: 398,505 out of 33,775,569
Identity over aligned base-pairs: 64.8%

Setaria italica

Uncovered: 374,798,111 out of 405,732,883
Covered: 30,934,772 out of 405,732,883

Uncovered: 18,703,830 out of 39,583,990
Matches: 13,390,184 out of 39,583,990
Mismatches: 6,991,134 out of 39,583,990
Insertions: 498,842 out of 39,583,990
Identity over aligned base-pairs: 64.1%

Block size distribution

Size range All 118,568 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
870
4.5 kb
10 bp - 100 bp
18,038
1.2 Mb
3,190
226.0 kb
100 bp - 1 kb
92,786
30.9 Mb
23,789
10.1 Mb
1 kb - 10 kb
6,874
10.0 Mb
15,350
31.5 Mb
10 kb - 100 kb
35
429.1 kb