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 F2 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,350,381 |
G→C |
G457G (GGC→GGG) |
cadC ← |
lysine decarboxylation/transport transcriptional activator CadC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,350,381 | 0 | G | C | 100.0%
| 73.3
/ NA
| 23 | G457G (GGC→GGG) | cadC | lysine decarboxylation/transport transcriptional activator CadC |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base C (7/16); total (7/16) |
TGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350299‑4350465
|
tgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa < 1:117139/90‑1 (MQ=255)
tgtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCa > 2:383075/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa > 2:273778/1‑90 (MQ=255)
gtTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCaa < 1:492431/90‑1 (MQ=255)
ccTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATaa > 2:554120/1‑90 (MQ=255)
tGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 2:2381/90‑1 (MQ=255)
gggCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt > 1:30250/1‑89 (MQ=255)
gggCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAAtt < 2:30250/89‑1 (MQ=255)
ttAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGAc < 2:177192/90‑1 (MQ=255)
cGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCaa < 1:82165/90‑1 (MQ=255)
atGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca > 2:57802/1‑59 (MQ=255)
atGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAAcaca < 1:57802/59‑1 (MQ=255)
aGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTAtt > 2:92969/1‑90 (MQ=255)
tgctTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTAt < 2:63631/90‑1 (MQ=255)
ttCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGc < 1:39202/90‑1 (MQ=255)
ttCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGc < 1:351709/90‑1 (MQ=255)
cccGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCt < 1:554120/90‑1 (MQ=255)
tCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACt > 1:297328/1‑90 (MQ=255)
cTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATc < 1:152596/90‑1 (MQ=255)
ttcatAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGtttt < 2:297328/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCGAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:273778/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTGTCGCCTGGTAAGACTCATCTGttttacctttt < 1:228091/90‑1 (MQ=255)
aCCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGttttacctttt < 1:546672/90‑1 (MQ=255)
|
TGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTT > NZ_CP009273/4350299‑4350465
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350286‑4350475
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAA < SRR3722092.194635/100‑1 (MQ=60)
cgtcggcagcgtcagatgtgtataagagacAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACAC < SRR3722092.559254/70‑1 (MQ=60)
TGTTTGCCAATGGGTGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATT < SRR3722092.119128/100‑1 (MQ=60)
GTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTT > SRR3722092.30772/1‑100 (MQ=60)
GTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTT < SRR3722092.502225/100‑1 (MQ=60)
tcagatgtgtataagagacAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCC < SRR3722092.58739/81‑1 (MQ=60)
cgagatctacactaagatggtcgtcggcagcgtcagatgtgtataagagacagTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAG < SRR3722092.351815/47‑1 (MQ=60)
CGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCC < SRR3722092.83568/100‑1 (MQ=60)
TTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGAC < SRR3722092.358098/100‑1 (MQ=60)
TTCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGAC < SRR3722092.39885/100‑1 (MQ=60)
TCCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACT > SRR3722092.302542/1‑100 (MQ=60)
CCCGGTTCATCCCCTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTC < SRR3722092.565235/100‑1 (MQ=60)
CTTCATTTCATAAACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCT < SRR3722092.155161/100‑1 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCGAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722092.278404/100‑1 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTGTCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722092.231823/100‑1 (MQ=60)
ACCTTCCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC < SRR3722092.557645/100‑1 (MQ=60)
|
ATCCAGTAAAGGGTGTTTGCCCCTGGGCGTAAATTAAAGGCGGTGAGATATGCATCAGCTGCTTCCCGGTTCATCCCCTTCATTTCATAAACCTTGCCAAGCAACACATAATTTAGCCAGGACATTTCAAGATCAATGCCAGTATTTATCGCCTGGTAAGACTCATCTGTTTTACCTTTTACCAGAGCAC > NZ_CP009273/4350286‑4350475
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
