Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F1 I1 R1
|
150 |
26.0 |
2053212 |
90.0% |
1847890 |
107.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
AM260479 |
1,089,440 |
Δ1 bp |
intergenic (+115/‑17) |
h16_A0996 → / → h16_A0997 |
FAD/FMN‑containing dehydrogenase/conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | AM260479 | 1,089,439 | 0 | C | . | 100.0%
| 47.8
/ NA
| 12 | intergenic (+114/‑18) | h16_A0996/h16_A0997 | FAD/FMN‑containing dehydrogenase/conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (5/7); total (5/7) |
TGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCG > AM260479/1089327‑1089548
|
tGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGcagatcagat > 1:711540/1‑131 (MQ=255)
aGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCa < 2:905361/134‑1 (MQ=255)
aGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACaa > 1:244982/1‑134 (MQ=255)
gggCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc < 1:120309/134‑1 (MQ=255)
gggCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc < 2:18973/134‑1 (MQ=255)
ggTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt < 2:711540/134‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGcc > 2:239125/1‑133 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCg < 2:244982/134‑1 (MQ=255)
cgcgGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAag < 1:239125/134‑1 (MQ=255)
gAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAag > 1:492391/1‑112 (MQ=255)
gAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAag < 2:492391/112‑1 (MQ=255)
tATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACcg > 1:316903/1‑134 (MQ=255)
|
TGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCG > AM260479/1089327‑1089548
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCACCTGGACG > AM260479/1089297‑1089589
|
ACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGA < GWNJ‑0478:712:GW2002102894th:2:2108:9380:33392/150‑1 (MQ=60)
tatttattttttttttttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAG < GWNJ‑0478:712:GW2002102894th:2:2211:6176:49587/56‑1 (MQ=60)
CAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATC < GWNJ‑0478:712:GW2002102894th:2:1103:4639:7621/150‑1 (MQ=60)
ATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATG > GWNJ‑0478:712:GW2002102894th:2:2112:18460:73361/1‑147 (MQ=60)
GCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAC > GWNJ‑0478:712:GW2002102894th:2:1116:12323:45956/1‑150 (MQ=60)
AGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTAC < GWNJ‑0478:712:GW2002102894th:2:1108:20577:98553/150‑1 (MQ=60)
ACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAAC < GWNJ‑0478:712:GW2002102894th:2:1116:9447:9480/150‑1 (MQ=60)
GCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACctgtctct > GWNJ‑0478:712:GW2002102894th:2:1214:17271:70703/1‑142 (MQ=60)
ATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGC > GWNJ‑0478:712:GW2002102894th:2:1204:17232:36115/1‑150 (MQ=60)
GTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACctgtctcttatacacatctccgagcccacgagacggagct > GWNJ‑0478:712:GW2002102894th:2:1207:4942:61328/1‑109 (MQ=60)
CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCACCTGGACG > GWNJ‑0478:712:GW2002102894th:2:1216:18905:71381/1‑150 (MQ=60)
CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCACCTGGACG > GWNJ‑0478:712:GW2002102894th:2:2208:18437:38882/1‑150 (MQ=60)
|
ACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCGAGGCCTTCGGCGATCCGGTGCACCTGGACG > AM260479/1089297‑1089589
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
