HTML output example

MIRA creates a lot of result files, supporting all the major relevant output formats of sequence assemblies. Below is an example of HTML output generated by MIRA.

Project step3_out.caf

Tag legend

= MISM; Mismatch (discrepancy) between reads and consensus

= PRMB; Probable Repeat Marker Base set by MIRA

= WRMB; Weak Repeat Marker Base set by MIRA

= PROS; Possible inteR Organism SNP set by MIRA

= PAOS; Possible intrA Organism SNP set by MIRA

= PIOS; Possible Inter- and intra-Organism SNP set by MIRA

= POLY; Poly-A or Poly-T site set by MIRA

= EDxD; Delete operation set by EdIt

= EDxI; Insert operation set by EdIt

= EDxC; Change operation set by EdIt

= IUPAC; IUPAC base (shows only in HTML output)

Contig List

Contig 1 (495)

stdname_c1

Statistics

Contig id: 1
Contig length: 495
Avg. contig coverage: 3.78
Consensus contains: A: 125 C: 109 G: 137 T: 93 N: 0 *: 2

Num reads: 4
Avg. read length: 469
Reads contain 1867 bases, 0 Ns and 9 gaps.

Contig

0
| . | . | . | . | . | .

strain1_c1+ TTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCTCAAAATGCCGGCGGGTCACGGTT

strain2_c1- TTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCGCAAAATGCCGGCGGGTCACGGTT

strain2_s2- GTGAACAAGGCA*G*CTGAAAAACACCTCAAAATGCCGGCGGGTCACGGTT

Consensus: TTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCKCAAAATGCCGGCGGGTCACGGTT

60
| . | . | . | . | . | .

strain1_c1+ TGAGGTCACGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATC

strain2_c1- TGGGGTCGCGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATC

strain2_s2- TGAGTTCACGCACCAGGGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATC

strain1_s2- CGGCCATTCAGGAAGAAGGGTCCTACCCATC

Consensus: TGRGGTCRCGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATC

120
| . | . | . | . | . | .

strain1_c1+ TCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGT

strain2_c1- TCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGT

strain2_s2- TCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGT

strain1_s2- TCACAACTTACCTTCGTATCTTCAAAGTCGCCGACTATGTTGATGTCAAGGTTAACGGGT

Consensus: TCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGT

180
| . | . | . | . | . | .

strain1_c1+ CGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGCCGCACGGGTCGGGTATGGAACG

strain2_c1- CGATCCACAAAGGTATGCCCCACAAGTTCTATCATGGCCGCACGGGTCGGGTATGGAACG

strain2_s2- CGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGGCGCACGGGTCGGGTCTGGAATG

strain1_s2- CGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGGCGCACGGGTCGGGTATGGAACG

Consensus: CGATCCACAAAGGTATGCCCCACAAGTTCTAYCATGGSCGCACGGGTCGGGTMTGGAAYG

240
| . | . | . | . | . | .

strain1_c1+ TCACCAAGCGCGCTGTTGGTGTTGAGGTCAACAAGCAGGTTGGAAACAGAATCATAAGGA

strain2_c1- TCACCAAGCGTGCTGTTGGTGTTGAGGTCAACAAGCAGGTTGGAAACAGAATCATAAGGA

strain2_s2- TTACCAAGCGCGCTGTTGGTGTTGAGGTCAACAAACAGGTTGGTAACAGGATCATAAGGA

strain1_s2- TCACCAAGCGCGCTGTTGGTGTTGAGGTCAACAAGCAGGTTGGAAACAGAATCATAAGGA

Consensus: TYACCAAGCGYGCTGTTGGTGTTGAGGTCAACAARCAGGTTGGWAACAGRATCATAAGGA

300
| . | . | . | . | . | .

strain1_c1+ AGAGGATTCATGTTCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGG

strain2_c1- AGAGGATTCATGTTCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGG

strain2_s2- AGAGGATTCATGTTCGTGTGGAACATGTCCAGCCATCTCGTTGCCATGAGGAGATAATGG

strain1_s2- AGAGGATTCATGTTCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGG

Consensus: AGAGGATTCATGTTCGTGTGGAACATGTCCAGCCATCWMGKTGCCATGAGGAGATMATGG

360
| . | . | . | . | . | .

strain1_c1+ AGAGGATCAAGAAGAACGATAAGTTGAAGGCTGAGGCCAAGGCACAAGGTAAGATTATCA

strain2_c1- AGAGGATCAAGAAGAACGATAAGTTGAAGGCTGAGGCCAAGGCACAAGGTAAGATTATCA

strain2_s2- AGAGGATCAAGAAGAATGATAAGTTGAAGGCTGAGGCAAAGGCACAGGGAAAGATTATCA

strain1_s2- AGAGGATCAAGAAGAACGATAAGTTGAAGGCTGAGGCCAAGGCACAAGGTAAGATTATCA

Consensus: AGAGGATCAAGAAGAAYGATAAGTTGAAGGCTGAGGCMAAGGCACARGGWAAGATTATCA

420
| . | . | . | . | . | .

strain1_c1+ GCACCAAGAGACAGCCAGAGGGACCCAAGCCTGGTTTCATGGTGCAGGGTACCTCGGCC*

strain2_c1- GCACCAAGAGACAGCCAGAGGGACCCAAGCCTGGTTTCATGGTAGAGGGTACCTCGGCC*

strain2_s2- GCACCAAGAGGCAGCCTGAGGGACCCAAGCCTGGTTTCATGGTGGAGGGTACCT*GCCCG

strain1_s2- GCACCAAGAGACAGCCAGAGGGACCCAAGCCTGGTTTCATGGTAGAGGGTACCTCGGCC*

Consensus: GCACCAAGAGRCAGCCWGAGGGACCCAAGCCTGGTTTCATGGTRSAGGGTACCTCGSCC*

480
|    .    |    .    |    .    |    .    |    .    |    .

strain1_c1+ *GCGACCACAA

strain2_c1- *GCGACCACGCTAA

strain2_s2- GGCGGCCGCTCGAAA

strain1_s2- *GCGACCACGCTAA

Consensus: *GCGRCCRCKCKAAA