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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,015,451 |
C→G |
16.6% |
G206G (GGG→GGC) |
fumA ← |
aerobic Class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,015,451 | 0 | C | G | 16.6%
| 123.8
/ 16.0
| 54 | G206G (GGG→GGC) | fumA | aerobic Class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base C (25/20); new base G (2/7); total (27/27) |
| Fisher's exact test for biased strand distribution p-value = 1.42e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
ATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGC > minE/1015388‑1015519
|
aTACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCg < 1:3422075/71‑1 (MQ=255)
aCGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTccc < 1:2724711/64‑1 (MQ=255)
cGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt > 1:3333164/1‑69 (MQ=255)
cGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGt > 1:2216414/1‑69 (MQ=255)
ggCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCtt < 1:1545850/71‑1 (MQ=255)
gccgccGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGc < 1:3165892/68‑1 (MQ=255)
cgccgTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCtt < 1:2783463/68‑1 (MQ=255)
cgTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGttt < 1:756110/71‑1 (MQ=255)
gTACCGAGGGTACGCATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTc < 1:802988/71‑1 (MQ=255)
tACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGt < 1:2957101/56‑1 (MQ=255)
tACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTcc > 1:2133629/1‑71 (MQ=255)
cAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTATCCTGAt < 1:1437798/71‑1 (MQ=255)
aGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa > 1:3924993/1‑69 (MQ=255)
gCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa > 1:3683308/1‑68 (MQ=255)
gCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGa > 1:2826789/1‑68 (MQ=255)
cGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATag < 1:961320/70‑1 (MQ=255)
tacgcATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTa > 1:429865/3‑67 (MQ=255)
tacgcATTTTCTCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAgaga < 1:1089364/69‑1 (MQ=255)
gcgcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCa > 1:1995983/1‑44 (MQ=255)
gcgcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAgaga > 1:2117039/1‑70 (MQ=255)
gcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCtt < 1:72174/51‑1 (MQ=255)
gcATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCtt < 1:246406/51‑1 (MQ=255)
cATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCtt < 1:2898833/50‑1 (MQ=255)
aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt > 1:773441/1‑71 (MQ=255)
aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt > 1:928590/1‑71 (MQ=255)
aTCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGt > 1:1650343/1‑71 (MQ=255)
ttttctCGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTc < 1:1852119/53‑1 (MQ=255)
tcttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTg < 1:451989/58‑1 (MQ=255)
cttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTc > 1:2744265/1‑54 (MQ=255)
cttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt > 1:2457701/1‑71 (MQ=255)
cttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCt > 1:947164/1‑71 (MQ=255)
ttctCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCtt > 1:770460/1‑71 (MQ=255)
ctcGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTg < 1:486537/70‑1 (MQ=255)
ctcGACGAGGAAGTTTTTCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTg < 1:3394272/70‑1 (MQ=255)
ctcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGt > 1:1384873/1‑71 (MQ=255)
tcAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGtt > 1:2938573/1‑71 (MQ=255)
cAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCttt > 1:1855221/1‑43 (MQ=255)
aaCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTg > 1:109881/1‑71 (MQ=255)
aCCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATa < 1:3360637/53‑1 (MQ=255)
ggTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTg < 1:2346197/46‑1 (MQ=255)
gTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTg < 1:1585827/61‑1 (MQ=255)
aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGttt > 1:1472822/1‑62 (MQ=255)
aaTTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGttt > 1:2359568/1‑62 (MQ=255)
gtttttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAgccgc < 1:1590002/70‑3 (MQ=255)
tttttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccacc < 1:678444/71‑1 (MQ=255)
ttttCAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAgccgccg > 1:1557771/1‑70 (MQ=255)
tttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccac > 1:557730/1‑71 (MQ=255)
ttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTc < 1:3827191/51‑1 (MQ=255)
ttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTc < 1:3466461/51‑1 (MQ=255)
ttCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAaccaccacc > 1:2378811/1‑71 (MQ=255)
cAGTTTGCCGGGAGTCAGCAGGGCTTTGGTTTCCTGGTAGAGATACGTTTTGTTGGCAGAGCCGCCGCCt < 1:1077067/70‑1 (MQ=255)
cAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACg < 1:3932005/47‑1 (MQ=255)
aGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATa < 1:2934391/38‑1 (MQ=255)
ttCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc > 1:349173/1‑71 (MQ=255)
tCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGc > 1:3921911/1‑70 (MQ=255)
|
ATACGGAGGACAGGCCGCCGTACCCAGCGTGCGCATCTTCTCAACCAGGTAATTTTTCAGTTTCCCCGGCGTCAGTAACGCTTTGGTTTCCTGATAGAGATACGTCTTGTTTGCCGAACCACCACCTTTGGC > minE/1015388‑1015519
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
