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Triticum aestivum vs Setaria italica LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Setaria italica (Setaria italica, Setaria_italica_v2.0) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 106. Triticum aestivum 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

ParameterTriticum aestivumSetaria italica
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 980,502 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Triticum aestivum

Uncovered: 14,074,269,790 out of 14,547,261,565
Covered: 472,991,775 out of 14,547,261,565

Uncovered: 12,261,534 out of 133,674,966
Matches: 93,171,641 out of 133,674,966
Mismatches: 25,466,179 out of 133,674,966
Insertions: 2,775,612 out of 133,674,966
Identity over aligned base-pairs: 76.7%

Setaria italica

Uncovered: 294,678,556 out of 405,732,883
Covered: 111,054,327 out of 405,732,883

Uncovered: 3,647,112 out of 39,583,990
Matches: 27,470,124 out of 39,583,990
Mismatches: 7,466,506 out of 39,583,990
Insertions: 1,000,248 out of 39,583,990
Identity over aligned base-pairs: 76.4%

Block size distribution

Size range All 980,502 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
6,787
36.9 kb
10 bp - 100 bp
133,277
8.7 Mb
65,258
4.5 Mb
100 bp - 1 kb
686,802
259.5 Mb
342,044
123.1 Mb
1 kb - 10 kb
153,391
274.4 Mb
143,734
365.8 Mb
10 kb - 100 kb
245
2.9 Mb
3,479
51.7 Mb
100 kb - 1 Mb
3
328.6 kb