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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,852,078 |
T→G |
T467P (ACG→CCG) |
yidK ← |
solute:sodium symporter family transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,852,078 | 0 | T | G | 82.5%
| 107.9
/ 15.0
| 40 | T467P (ACG→CCG) | yidK | solute:sodium symporter family transporter |
| Reads supporting (aligned to +/- strand): ref base T (4/3); new base G (12/21); total (16/24) |
| Fisher's exact test for biased strand distribution p-value = 4.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.73e-01 |
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC > NZ_CP009273/3851991‑3852162
|
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 1:792566/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:637160/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTAAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:327021/90‑1 (MQ=255)
gCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAg > 2:43710/1‑90 (MQ=255)
aaaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGc < 1:501171/90‑1 (MQ=255)
aaaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGc < 2:642883/90‑1 (MQ=255)
aaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGcc < 1:290047/90‑1 (MQ=255)
aaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGcc < 2:794254/90‑1 (MQ=255)
gCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGc < 1:659754/90‑1 (MQ=255)
gCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGc < 2:591240/90‑1 (MQ=255)
aTCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGcac > 2:585088/1‑90 (MQ=255)
aTCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGcac > 2:520882/1‑90 (MQ=255)
ttGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATag < 2:490780/90‑1 (MQ=255)
ttGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATag < 1:335080/90‑1 (MQ=255)
ggTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGaa > 1:579784/1‑90 (MQ=255)
tGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAAt > 2:255114/1‑90 (MQ=255)
gAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATg > 2:651333/1‑90 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCg > 2:829817/1‑90 (MQ=255)
gcgcgcGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAAc < 1:57718/90‑1 (MQ=255)
gcgcgcGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAAc < 1:668418/90‑1 (MQ=255)
cgcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTc < 1:829817/90‑1 (MQ=255)
gcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCa > 1:290564/1‑90 (MQ=255)
cgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCAc > 2:630848/1‑90 (MQ=255)
cgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCAc < 2:365930/90‑1 (MQ=255)
cgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCAc < 1:203602/90‑1 (MQ=255)
ttGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGa < 2:95446/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 2:391962/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 2:85872/90‑1 (MQ=255)
aCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAt > 1:386992/1‑90 (MQ=255)
aTCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTg > 2:385680/1‑90 (MQ=255)
tCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGa > 2:596089/1‑90 (MQ=255)
cACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGAt < 1:331863/90‑1 (MQ=255)
gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc > 2:622875/1‑90 (MQ=255)
aCGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt < 1:402489/90‑1 (MQ=255)
ccACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGc < 1:637237/90‑1 (MQ=255)
aCGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGt < 2:177229/46‑1 (MQ=255)
aCGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGt > 1:177229/1‑46 (MQ=255)
aCGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCa > 2:299158/1‑90 (MQ=255)
tGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCa < 2:110931/90‑1 (MQ=255)
gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGc > 1:58759/1‑90 (MQ=255)
|
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC > NZ_CP009273/3851991‑3852162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGCCGCCA > NZ_CP009273/3851979‑3852176
|
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGG > SRR3722079.4376/1‑100 (MQ=60)
TCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACA < SRR3722079.234966/100‑1 (MQ=60)
TCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACA < SRR3722079.688808/100‑1 (MQ=60)
GTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCC < SRR3722079.667596/100‑1 (MQ=60)
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC < SRR3722079.801062/100‑1 (MQ=60)
AAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAG < SRR3722079.505670/100‑1 (MQ=60)
AACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGA < SRR3722079.292441/100‑1 (MQ=60)
ggcatacgagatcctctctggtctcgtgggctcggagatgtgtataagagaCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGG < SRR3722079.757739/49‑1 (MQ=60)
GCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGA < SRR3722079.666606/100‑1 (MQ=60)
CATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAA > SRR3722079.585523/1‑100 (MQ=60)
TTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGA < SRR3722079.337735/100‑1 (MQ=60)
GGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCA > SRR3722079.292960/1‑100 (MQ=60)
GCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAT < SRR3722079.675395/100‑1 (MQ=60)
GCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAT < SRR3722079.58177/100‑1 (MQ=60)
CGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGT < SRR3722079.838697/100‑1 (MQ=60)
CGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTG < SRR3722079.205361/100‑1 (MQ=60)
GTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAT > SRR3722079.390182/1‑100 (MQ=60)
CACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATT < SRR3722079.334506/100‑1 (MQ=60)
CATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCtgtctcttatacacatctccgagcccacgagac > SRR3722079.178775/1‑67 (MQ=60)
ACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCC < SRR3722079.405893/100‑1 (MQ=60)
CCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCAT < SRR3722079.643797/100‑1 (MQ=60)
CGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC > SRR3722079.59231/1‑100 (MQ=60)
GGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGCCGCCA > SRR3722079.169092/1‑100 (MQ=60)
|
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGCCGCCA > NZ_CP009273/3851979‑3852176
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
