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 |
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 | 93.5%
| 96.4
/ ‑1.5
| 31 | T467P (ACG→CCG) | yidK | solute:sodium symporter family transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base G (12/17); total (13/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC > NZ_CP009273/3851991‑3852162
|
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:173842/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:7117/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:230384/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:134102/90‑1 (MQ=255)
cGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAg < 1:332754/90‑1 (MQ=255)
gCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGc < 2:518620/90‑1 (MQ=255)
gCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGc < 1:148779/90‑1 (MQ=255)
aaGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAgg < 2:432865/90‑1 (MQ=255)
gAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAg < 1:269468/75‑1 (MQ=255)
gAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAg > 2:269468/1‑75 (MQ=255)
gAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATg > 2:479726/1‑90 (MQ=255)
ttGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGa < 2:175175/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 1:323081/90‑1 (MQ=255)
aaaaCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGtt < 2:406328/90‑1 (MQ=255)
aCCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAt > 1:382723/1‑90 (MQ=255)
aCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAt > 1:564818/1‑90 (MQ=255)
gATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTc < 1:431166/66‑1 (MQ=255)
gATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTc > 2:431166/1‑66 (MQ=255)
aTCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTg > 2:139392/1‑90 (MQ=255)
gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc > 1:464417/1‑90 (MQ=255)
gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc < 1:512698/90‑1 (MQ=255)
aCGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt < 2:382723/90‑1 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc > 2:363493/1‑79 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc < 1:363493/79‑1 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt > 1:294851/1‑84 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt < 2:294851/84‑1 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCa > 2:216147/1‑90 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCa > 1:98984/1‑90 (MQ=255)
ttGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAAc > 2:304848/1‑48 (MQ=255)
ttGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAAc < 1:304848/48‑1 (MQ=255)
gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGc > 2:543111/1‑90 (MQ=255)
|
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGC > NZ_CP009273/3851991‑3852162
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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 > SRR3722092.529016/1‑100 (MQ=60)
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGG > SRR3722092.176745/1‑100 (MQ=60)
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGG > SRR3722092.528360/1‑100 (MQ=60)
TCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACA < SRR3722092.105642/100‑1 (MQ=60)
gccagCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGG < SRR3722092.273989/95‑1 (MQ=60)
CGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGG < SRR3722092.338639/100‑1 (MQ=60)
GCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGA < SRR3722092.151282/100‑1 (MQ=60)
tgtataagagacagTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACC < SRR3722092.439552/86‑1 (MQ=60)
cgtcggcagcgtcagatgtgtataagagacagCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAT < SRR3722092.310215/68‑1 (MQ=60)
GTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAT > SRR3722092.389996/1‑100 (MQ=60)
GTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAT > SRR3722092.576135/1‑100 (MQ=60)
TGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGT < SRR3722092.328807/100‑1 (MQ=60)
CCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGC > SRR3722092.473615/1‑100 (MQ=60)
GCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCC < SRR3722092.370249/100‑1 (MQ=60)
GCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCC < SRR3722092.522983/100‑1 (MQ=60)
CATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCA > SRR3722092.300006/1‑100 (MQ=60)
CATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCA > SRR3722092.100679/1‑100 (MQ=60)
AGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGC > SRR3722092.244885/1‑100 (MQ=60)
GGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGCCGCCA > SRR3722092.560558/1‑100 (MQ=60)
|
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTACTTTTGCCGCCA > NZ_CP009273/3851979‑3852176
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
