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Mouse vs Norway rat - BN/NHsdMcwi LastZ results

Mouse (Mus musculus, GRCm39) and Norway rat - BN/NHsdMcwi (Rattus norvegicus, GRCr8) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 114. Mouse 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

ParameterMouseNorway rat - BN/NHsdMcwi
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 1,818,665 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Mouse

Uncovered: 770,315,916 out of 2,728,222,451
Covered: 1,957,906,535 out of 2,728,222,451

Uncovered: 136,866 out of 36,936,991
Matches: 33,917,441 out of 36,936,991
Mismatches: 2,757,949 out of 36,936,991
Insertions: 124,735 out of 36,936,991
Identity over aligned base-pairs: 92.2%

Norway rat - BN/NHsdMcwi

Uncovered: 1,031,424,110 out of 2,849,597,492
Covered: 1,818,173,382 out of 2,849,597,492

Uncovered: 2,066,415 out of 37,775,112
Matches: 33,031,837 out of 37,775,112
Mismatches: 2,547,882 out of 37,775,112
Insertions: 128,978 out of 37,775,112
Identity over aligned base-pairs: 92.5%

Block size distribution

Size range All 1,818,665 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
39,885
248.4 kb
10 bp - 100 bp
199,360
10.8 Mb
39,224
2.6 Mb
100 bp - 1 kb
916,677
413.0 Mb
106,896
36.8 Mb
1 kb - 10 kb
659,098
1.6 Gb
29,838
78.5 Mb
10 kb - 100 kb
3,631
47.0 Mb
2,353
52.4 Mb
100 kb - 1 Mb
14
1.9 Mb
65
17.4 Mb
1 Mb - 10 Mb
32
132.3 Mb
10 Mb - 100 Mb
32
1.3 Gb
100 Mb - 1 Gb
4
445.1 Mb