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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
365,796 |
T→C |
39.0% |
K532K (AAA→AAG) |
fepA ← |
iron‑enterobactin outer membrane transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 365,796 | 0 | T | C | 39.0%
| 15.0
/ 25.2
| 41 | K532K (AAA→AAG) | fepA | iron‑enterobactin outer membrane transporter |
| Reads supporting (aligned to +/- strand): ref base T (4/21); new base C (7/9); total (11/30) |
| Fisher's exact test for biased strand distribution p-value = 7.43e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTGG > minE/365733‑365860
|
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGATCAATCTCTttgtt < 1:1346338/69‑1 (MQ=255)
aTCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:1304709/69‑1 (MQ=255)
tCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:536229/68‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:52527/51‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt > 1:145905/1‑51 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt < 1:29644/51‑1 (MQ=255)
gACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTttgtt > 1:2626558/1‑51 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:752563/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:400790/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:3209459/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:3206790/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:3170796/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:258116/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:2370618/69‑1 (MQ=255)
aCGCCCGCCAGCCAACCGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:232792/69‑1 (MQ=255)
cgccAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTc < 1:394816/69‑1 (MQ=255)
cgccAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTc < 1:2614331/69‑1 (MQ=255)
cgccAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTc < 1:1203559/69‑1 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGttt > 1:3269144/2‑47 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATcat > 1:2459268/2‑63 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATcat > 1:2773729/2‑63 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATcat > 1:245442/2‑63 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATcat > 1:2126389/2‑63 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATca > 1:231958/2‑63 (MQ=255)
accGTCGCGTTTGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTCAGGTCATca > 1:2673293/2‑63 (MQ=255)
gcgTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTc < 1:2474996/54‑1 (MQ=255)
tttGAACTCCAGACCAATCTCCTTGTTGATGCTGGTTTCTGCTTTc < 1:318685/46‑1 (MQ=255)
tGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATagc > 1:308232/1‑69 (MQ=255)
tGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATagc > 1:3358182/1‑69 (MQ=255)
tGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATagc < 1:2089850/69‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:732373/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:1400866/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:1061080/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:3232758/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:1635409/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:2227474/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:2637614/45‑1 (MQ=255)
ccAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCAt < 1:258670/45‑1 (MQ=255)
tctcTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg < 1:617527/69‑1 (MQ=255)
tctcTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg < 1:251482/69‑1 (MQ=255)
tctcTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg < 1:2453522/69‑1 (MQ=255)
ctctTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGtt > 1:3113259/1‑39 (MQ=255)
ctctTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg > 1:3326580/1‑68 (MQ=255)
ctctTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg > 1:399054/1‑68 (MQ=255)
ctctTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTgg > 1:1540337/1‑68 (MQ=255)
|
ATCGTTACGGAACCAGGTGACGCCCGCCAGCCACCCGTCGCGTTTGAACTCCAGACCAATCTCTTTGTTGATGCTGGTTTCTGCTTTCAGGTCATCGTTACCTTGCAGATAGCAGCCGCCCGCGCTGG > minE/365733‑365860
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
