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 F3 I0 R2
|
232 |
76.3 |
4135488 |
90.9% |
3759158 |
60.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
623,375 |
C→T |
34.0% |
T19I (ACC→ATC) |
msbA → |
fused lipid transporter subunits and membrane component and ATP‑binding component of ABC superfamily |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 623,375 | 0 | C | T | 34.0%
| 60.6
/ 48.6
| 53 | T19I (ACC→ATC) | msbA | fused lipid transporter subunits and membrane component and ATP‑binding component of ABC superfamily |
| Reads supporting (aligned to +/- strand): ref base C (25/10); new base T (7/11); total (32/21) |
| Fisher's exact test for biased strand distribution p-value = 3.70e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.91e-01 |
TGGTTTTTTGAATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATAC > minE/623309‑623444
|
tGGTTTTTTGAATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCAtt > 1:3295314/1‑71 (MQ=255)
ttttGAATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGcc > 1:65021/1‑71 (MQ=255)
ttttGAATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGcc > 1:2205538/1‑71 (MQ=255)
tGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCa > 1:1051990/1‑69 (MQ=255)
tGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCa > 1:1207181/1‑69 (MQ=255)
tGCATAACGACAAAGATCTCTCTACGTGGCAGAAATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCa > 1:3667909/1‑69 (MQ=255)
cATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGc < 1:1829105/71‑1 (MQ=255)
aCGATAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGt > 1:1324718/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGt > 1:3067776/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGt > 1:3641639/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGt > 1:2345073/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGt > 1:1482690/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCAt > 1:1626316/1‑52 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCaa < 1:1789794/64‑1 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCaa < 1:3170154/64‑1 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGt > 1:736708/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGt > 1:3352112/1‑71 (MQ=255)
aCGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGt > 1:3433670/1‑71 (MQ=255)
aCAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTg < 1:267851/71‑1 (MQ=255)
aCAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTg < 1:2991263/71‑1 (MQ=255)
cAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTg < 1:2074722/70‑1 (MQ=255)
aaaGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGTCTGAt > 1:3516795/1‑71 (MQ=255)
aaaGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGAt > 1:2370310/1‑71 (MQ=255)
cGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTggcgggcg > 1:3920280/1‑69 (MQ=255)
cGTGGCAGACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTggcgggcg < 1:3610841/69‑1 (MQ=255)
gCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGt > 1:697069/1‑71 (MQ=255)
cAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGGGGGTCTGATCGTGGCGGGCGTAGCGtt < 1:647461/71‑1 (MQ=255)
cAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGtt < 1:3942862/71‑1 (MQ=255)
cAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGtt < 1:2053666/71‑1 (MQ=255)
gACATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTaa < 1:1940094/71‑1 (MQ=255)
aCATTCCGCCGACTGTGGCCAATCATTGCGCCTTTCa < 1:172855/37‑1 (MQ=255)
aTTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCgg > 1:3800968/1‑41 (MQ=255)
aTTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATcc > 1:1959516/1‑71 (MQ=255)
aTTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATcc > 1:1095769/1‑71 (MQ=255)
ccgccgACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTgg > 1:1051118/1‑50 (MQ=255)
ccgccgACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTgg > 1:519143/1‑50 (MQ=255)
ccgccgACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc > 1:3559908/1‑70 (MQ=255)
ccgccgACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc > 1:582054/1‑70 (MQ=255)
cgccgACTGTGGCCAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCaa < 1:3978728/71‑1 (MQ=255)
aCTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTg < 1:2155493/37‑1 (MQ=255)
tgtgGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGcagc > 1:3281181/1‑70 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGTTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:3499282/57‑1 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:888139/57‑1 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:331259/57‑1 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:3690694/57‑1 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:1341624/57‑1 (MQ=255)
ccAATCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTc < 1:3040820/57‑1 (MQ=255)
cAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGAt < 1:2326224/71‑1 (MQ=255)
aaCCATTGCGCCTTTCAAAGCGGGTCTGATCGTggc > 1:3981305/1‑36 (MQ=255)
aaCCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATa > 1:462861/1‑71 (MQ=255)
aaCCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATa > 1:3786231/1‑71 (MQ=255)
aCCATTGCGCCTTTCAAAGCGGGTCTGATCGTggcg > 1:2438095/1‑36 (MQ=255)
aCCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATAc > 1:128272/1‑71 (MQ=255)
ccATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCaa > 1:1689574/1‑55 (MQ=255)
ccATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCaa > 1:2200208/1‑55 (MQ=255)
|
TGGTTTTTTGAATGCATAACGACAAAGATCTCTCTACGTGGCAGACATTCCGCCGACTGTGGCCAACCATTGCGCCTTTCAAAGCGGGTCTGATCGTGGCGGGCGTAGCGTTAATCCTCAACGCAGCCAGCGATAC > minE/623309‑623444
|
| 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
