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Triticum aestivum vs Triticum aestivum Sy Mattis LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Sy Mattis (Triticum aestivum, PGSBv2.1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 113. 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)5000
Threshold for gapped extension (L)5000
Threshold for alignments between gapped alignment blocks (H)3000
Masking count (M)10
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 aestivumTriticum aestivum Sy Mattis
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,547,538 alignment blocks

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

Uncovered: 2,177,190,567 out of 14,547,261,565
Covered: 12,370,070,998 out of 14,547,261,565

Uncovered: 2,573,348 out of 133,674,966
Matches: 129,698,239 out of 133,674,966
Mismatches: 1,261,096 out of 133,674,966
Insertions: 142,283 out of 133,674,966
Identity over aligned base-pairs: 98.9%

Triticum aestivum Sy Mattis

Uncovered: 2,520,671,988 out of 14,884,612,126
Covered: 12,363,940,138 out of 14,884,612,126

Uncovered: 8,232,342 out of 175,482,126
Matches: 165,525,563 out of 175,482,126
Mismatches: 1,576,601 out of 175,482,126
Insertions: 147,620 out of 175,482,126
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,547,538 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,402
91.2 kb
10 bp - 100 bp
249,596
13.7 Mb
104,644
6.3 Mb
100 bp - 1 kb
574,941
219.5 Mb
275,453
103.2 Mb
1 kb - 10 kb
396,175
1.5 Gb
133,952
365.6 Mb
10 kb - 100 kb
299,870
9.5 Gb
5,995
108.6 Mb
100 kb - 1 Mb
11,554
1.5 Gb
332
122.1 Mb
1 Mb - 10 Mb
159
538.4 Mb
10 Mb - 100 Mb
21
391.4 Mb
100 Mb - 1 Gb
23
11.1 Gb