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Triticum aestivum vs Triticum aestivum Jagger LastZ results

Triticum aestivum (Triticum aestivum, IWGSC) and Triticum aestivum Jagger (Triticum aestivum, PGSBv2.1) 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 Jagger
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,591,260 alignment blocks

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

Uncovered: 2,133,740,321 out of 14,547,261,565
Covered: 12,413,521,244 out of 14,547,261,565

Uncovered: 2,848,464 out of 133,674,966
Matches: 129,233,305 out of 133,674,966
Mismatches: 1,462,125 out of 133,674,966
Insertions: 131,072 out of 133,674,966
Identity over aligned base-pairs: 98.8%

Triticum aestivum Jagger

Uncovered: 2,098,502,148 out of 14,538,313,898
Covered: 12,439,811,750 out of 14,538,313,898

Uncovered: 8,207,826 out of 174,238,857
Matches: 164,398,809 out of 174,238,857
Mismatches: 1,483,728 out of 174,238,857
Insertions: 148,494 out of 174,238,857
Identity over aligned base-pairs: 99.0%

Block size distribution

Size range All 1,591,260 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
15,387
91.6 kb
10 bp - 100 bp
249,402
13.7 Mb
102,736
6.2 Mb
100 bp - 1 kb
562,577
213.0 Mb
271,316
99.4 Mb
1 kb - 10 kb
426,967
1.7 Gb
121,132
337.7 Mb
10 kb - 100 kb
328,675
9.8 Gb
5,753
107.9 Mb
100 kb - 1 Mb
8,252
1.0 Gb
553
201.1 Mb
1 Mb - 10 Mb
181
569.1 Mb
10 Mb - 100 Mb
23
420.1 Mb
100 Mb - 1 Gb
21
11.1 Gb