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
|
154 |
26.6 |
2069536 |
90.2% |
1866721 |
108.9 |
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%
| 100.5
/ NA
| 23 | 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 . (13/10); total (13/10) |
GTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGC > AM260479/1089322‑1089558
|
gTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacaggg < 2:808649/122‑5 (MQ=255)
gTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacaggg > 1:808649/1‑118 (MQ=255)
aCTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGcagatcagat < 2:996929/133‑1 (MQ=255)
gCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAc < 2:883003/134‑1 (MQ=255)
gCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag > 2:877510/1‑110 (MQ=255)
gCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag < 1:877510/110‑1 (MQ=255)
gACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCagag > 1:794928/1‑134 (MQ=255)
gCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacaggg < 1:664990/83‑5 (MQ=255)
gCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATccacaggg > 2:664990/1‑79 (MQ=255)
gggCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc > 2:338702/1‑134 (MQ=255)
gCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc > 1:605222/1‑132 (MQ=255)
ggTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt < 1:338702/134‑1 (MQ=255)
ggTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt < 2:605222/134‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag < 1:938736/74‑1 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag > 2:938736/1‑74 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt > 2:233771/1‑129 (MQ=255)
ccTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGt < 1:233771/129‑1 (MQ=255)
gCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag > 2:686491/1‑66 (MQ=255)
gCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGagag < 1:686491/66‑1 (MQ=255)
tttCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGAAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTacga > 1:781778/1‑134 (MQ=255)
cAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCgaa > 2:186930/1‑134 (MQ=255)
cAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCgaa < 1:186930/134‑1 (MQ=255)
gAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc > 2:531170/1‑87 (MQ=255)
gAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAAc < 1:531170/87‑1 (MQ=255)
gAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGCGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGgacga > 2:893658/1‑134 (MQ=255)
gACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAg > 1:699243/1‑134 (MQ=255)
cgcgTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGc > 1:522268/1‑132 (MQ=255)
|
GTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGC > AM260479/1089322‑1089558
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ 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
CACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCG > AM260479/1089296‑1089559
|
CACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAG < GWNJ‑0478:712:GW2002102894th:2:2109:3781:34375/150‑1 (MQ=60)
CATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATC > GWNJ‑0478:712:GW2002102894th:2:2202:13343:47663/1‑147 (MQ=60)
ccgtctcgtgggctcggagatgtgtataagagacagAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATG < GWNJ‑0478:712:GW2002102894th:2:2111:6931:75049/113‑1 (MQ=60)
ggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAC < GWNJ‑0478:712:GW2002102894th:2:2113:5498:3657/97‑1 (MQ=60)
atatgtagctccgtctcgtgggctcggagatgtgtataagagacaGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAC < GWNJ‑0478:712:GW2002102894th:2:2210:7577:65807/105‑1 (MQ=60)
aagagacaGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGAC < GWNJ‑0478:712:GW2002102894th:2:2206:11552:93520/141‑1 (MQ=60)
GGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGT > GWNJ‑0478:712:GW2002102894th:2:2203:2040:52903/1‑150 (MQ=60)
atttcgtgcttttttcttttctttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaggtatccaCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTG < GWNJ‑0478:712:GW2002102894th:2:2115:18565:63417/41‑1 (MQ=60)
GGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACG > GWNJ‑0478:712:GW2002102894th:2:2107:7471:99857/1‑148 (MQ=60)
tttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGG < GWNJ‑0478:712:GW2002102894th:2:1114:17440:36771/75‑1 (MQ=60)
cgtgggctcggagatgtgtataagagacagGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTAC < GWNJ‑0478:712:GW2002102894th:2:2101:4134:89335/117‑1 (MQ=60)
GGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGA < GWNJ‑0478:712:GW2002102894th:2:1207:7408:68316/150‑1 (MQ=60)
GGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGA < GWNJ‑0478:712:GW2002102894th:2:1114:4216:69888/150‑1 (MQ=60)
GGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGAAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGAC > GWNJ‑0478:712:GW2002102894th:2:2201:7422:62549/1‑150 (MQ=60)
GCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttctgcttgaaaaaa > GWNJ‑0478:712:GW2002102894th:2:2116:13631:34568/1‑77 (MQ=60)
GCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGAC < GWNJ‑0478:712:GW2002102894th:2:1112:4315:3138/150‑1 (MQ=60)
TGCGAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGC > GWNJ‑0478:712:GW2002102894th:2:2113:19350:75508/1‑150 (MQ=60)
GAGTATCGGCGCGACCGCGTTGTATCCA‑CAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCG > GWNJ‑0478:712:GW2002102894th:2:2101:6139:26483/1‑148 (MQ=60)
|
CACAACCACAACATCAATCCGGCGGCGTAACTGGCGTAATCTGCAGGGACAGGCAGGAAGGCGGGGCAGGGCGGGTGGCCTGCCCCGCTTTCACGCGGCTGCAATACCGGCATGCGAGTATCGGCGCGACCGCGTTGTATCCACCAGGGAGAGCAGATCAGATGAGACCGGGCGAAGCAGAGTTGGTGCGGCGCATCCACAACGAGGTGGCCGACTACTACGACGAAGAGATCGAACTGGAACTGGACGACCGCGAAGCCAGCG > AM260479/1089296‑1089559
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
