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Triticum aestivum vs Triticum aestivum Stanley LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Stanley (Triticum aestivum, PGSBv2.2) 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)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 Stanley
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,589,890 alignment blocks

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

Uncovered: 2,200,266,521 out of 14,547,261,565
Covered: 12,346,995,044 out of 14,547,261,565

Uncovered: 2,710,251 out of 133,674,966
Matches: 129,625,651 out of 133,674,966
Mismatches: 1,212,606 out of 133,674,966
Insertions: 126,458 out of 133,674,966
Identity over aligned base-pairs: 99.0%

Triticum aestivum Stanley

Uncovered: 2,115,538,954 out of 14,463,524,036
Covered: 12,347,985,082 out of 14,463,524,036

Uncovered: 8,332,659 out of 174,633,329
Matches: 164,702,448 out of 174,633,329
Mismatches: 1,458,370 out of 174,633,329
Insertions: 139,852 out of 174,633,329
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,589,890 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,626
93.6 kb
10 bp - 100 bp
251,174
13.7 Mb
101,768
6.1 Mb
100 bp - 1 kb
565,496
213.6 Mb
275,582
100.8 Mb
1 kb - 10 kb
425,942
1.7 Gb
120,464
334.8 Mb
10 kb - 100 kb
323,126
9.7 Gb
5,604
104.3 Mb
100 kb - 1 Mb
8,526
1.1 Gb
407
151.3 Mb
1 Mb - 10 Mb
143
486.0 Mb
10 Mb - 100 Mb
22
542.7 Mb
100 Mb - 1 Gb
21
11.0 Gb