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 |
|
A21 F117 I0 R1
|
36 |
24.6 |
540534 |
94.7% |
511885 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
1,672,590 |
G→T |
100% |
L135I (CTT→ATT) |
rpoD ← |
DNA‑directed RNA polymerase sigma subunit RpoD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 1,672,590 | 0 | G | T | 95.9%
| 60.7
/ ‑4.4
| 24 | L135I (CTT→ATT) | rpoD | DNA‑directed RNA polymerase sigma subunit RpoD |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base T (8/15); total (9/15) |
| Fisher's exact test for biased strand distribution p-value = 3.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.46e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGA > CP000730/1672453‑1672723
|
tCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCt > 1:262172/1‑141 (MQ=255)
gTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAATTGGAAGTTCGCTTCTGCAATTCTTGAttt < 1:131032/141‑1 (MQ=255)
cAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACtt < 2:59746/141‑1 (MQ=255)
cAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACtt < 2:254513/141‑1 (MQ=255)
aTTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGCATCTCATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTtcat < 1:61997/141‑1 (MQ=255)
tCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGACTTTGCTACTTCACCACCt > 2:27585/1‑141 (MQ=255)
cTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCaa < 2:101331/141‑1 (MQ=255)
aataaGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACg > 1:179572/1‑141 (MQ=255)
atTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTc > 2:34379/1‑141 (MQ=255)
gATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTtg < 1:55365/141‑1 (MQ=255)
aTCAAGGAATAACCTGCCACGACCTGCGTATCTTTTAGCAATACTTTCAACTTAACGTAAGTTCGCTTCTGCAATTCTTGTTGTTGCTACTTCAGCACCTTGTTCAATACGTTTTGCTAATTCGATTTCTTCTTGTGCGCt < 2:81195/141‑1 (MQ=255)
aTCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTCCAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGTTATTCCGATTTCTTCTTGTGCACt > 1:124773/1‑141 (MQ=255)
tACCACGCCCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCCCCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAacac < 2:166538/141‑1 (MQ=255)
aCCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACg < 2:255228/141‑1 (MQ=255)
ccACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGc < 1:152948/141‑1 (MQ=255)
aCCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAAt > 2:210385/1‑141 (MQ=255)
aCGTATCTTTTAGCAATACTTACGACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCCATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCt > 2:193700/1‑141 (MQ=255)
aCGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCt < 1:262224/141‑1 (MQ=255)
ttttAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGt > 1:267618/1‑141 (MQ=255)
aGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAATTCTTAATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACACCCATTTTCTTTAAGGTAAAt > 1:204995/1‑141 (MQ=255)
cTTACAACTAAACGGAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACt < 1:95148/141‑1 (MQ=255)
cTTACAACGAAACGTAAGTTCGCTTCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACt < 1:39046/141‑1 (MQ=255)
cgtgtGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTg < 2:156797/137‑1 (MQ=255)
tCTGCAATTCTTGATTTTGCTACTTCATCACCTTGTTCAATTCGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGa < 1:34379/141‑1 (MQ=255)
|
TCCTTTGTTAAAGTCAAATTTTTCAACAGCTTTAATAAGACCCATATTACCTTCTTGGATTAAATCAAGGAATAACATACCACGACCTACGTATCTTTTAGCAATACTTACAACTAAACGTAAGTTCGCTTCTGCAAGTCTTGATTTTGCTACTTCATCACCTTGTTCAATACGTTTGGCTAATTCGATTTCTTCTTGTGCACTTAATAAGTTAACACGCCCAATTTCTTTAAGGTACATACGAACTGGGTCATTTATTTTAACACCTGGA > CP000730/1672453‑1672723
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
