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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,728,678 |
T→C |
47.9% |
F18F (TTT→TTC) |
yfhD → |
predicted transglycosylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,728,678 | 0 | T | C | 47.9%
| 1.3
/ 107.3
| 73 | F18F (TTT→TTC) | yfhD | predicted transglycosylase |
| Reads supporting (aligned to +/- strand): ref base T (12/26); new base C (18/17); total (30/43) |
| Fisher's exact test for biased strand distribution p-value = 1.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
GAGAGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTGACCGTGCGG > minE/1728614‑1728747
|
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:548067/71‑1 (MQ=255)
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:4125214/71‑1 (MQ=255)
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:1581463/71‑1 (MQ=255)
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:3129821/71‑1 (MQ=255)
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:300367/71‑1 (MQ=255)
gagaGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTg < 1:2418947/71‑1 (MQ=255)
agagTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTgg < 1:3246290/71‑1 (MQ=255)
agagTTGCGTGTGAGCACAATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAGCCTTTCgg > 1:3260564/1‑66 (MQ=255)
ttGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTa > 1:524117/1‑71 (MQ=255)
ttGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTa > 1:3482462/1‑71 (MQ=255)
gCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTg < 1:3365552/64‑1 (MQ=255)
cGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAACCCTTTTGGCCTGGATTACg < 1:3512377/70‑1 (MQ=255)
cGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACg < 1:4146258/70‑1 (MQ=255)
cGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACg < 1:3024490/70‑1 (MQ=255)
tgAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGa > 1:1291108/1‑61 (MQ=255)
tgAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACt < 1:2784503/70‑1 (MQ=255)
aGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGc > 1:2716073/1‑71 (MQ=255)
gCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGc > 1:1898389/1‑70 (MQ=255)
cACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTgg > 1:2296418/1‑51 (MQ=255)
cACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGa < 1:3601053/71‑1 (MQ=255)
aCCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGTCCTg < 1:141801/54‑1 (MQ=255)
ccATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACt < 1:966318/64‑1 (MQ=255)
ccATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACt < 1:3987432/64‑1 (MQ=255)
cATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGAtt < 1:1583314/56‑1 (MQ=255)
aTTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGaaa > 1:2668745/1‑69 (MQ=255)
ttCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGa > 1:1664037/1‑52 (MQ=255)
tCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACa > 1:4031493/1‑69 (MQ=255)
tCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGa < 1:2994150/57‑1 (MQ=255)
tCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGa < 1:3287670/57‑1 (MQ=255)
cATTCTCCCCTGACTTATAACGAATTCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGtt > 1:1451311/1‑71 (MQ=255)
tCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGa > 1:1651598/1‑45 (MQ=255)
cccTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTg < 1:3233149/41‑1 (MQ=255)
cccTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGAt > 1:3219222/1‑71 (MQ=255)
cTGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTa > 1:1945360/1‑71 (MQ=255)
tGACTTATAACGAAATCAACGGGAAACCTTTCGGc < 1:2925469/35‑1 (MQ=255)
tGACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGa < 1:3274296/54‑1 (MQ=255)
gACTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTAcc > 1:1388928/1‑71 (MQ=255)
aCTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTAc < 1:1280734/69‑1 (MQ=255)
aCTTATAACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCt > 1:3379494/1‑71 (MQ=255)
ataACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGAt < 1:204931/62‑1 (MQ=255)
ataACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTa > 1:341939/1‑64 (MQ=255)
ataACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGaa > 1:1740872/1‑41 (MQ=255)
ataACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTa > 1:649100/1‑64 (MQ=255)
taACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTg < 1:347417/43‑1 (MQ=255)
taACGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACt > 1:1934304/1‑42 (MQ=255)
aaCGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGaa < 1:2306957/47‑1 (MQ=255)
aaCGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGaa < 1:1683383/47‑1 (MQ=255)
aCGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGt > 1:2145044/1‑70 (MQ=255)
cGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaa < 1:1632021/71‑1 (MQ=255)
cGAAATCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAAc > 1:994486/1‑47 (MQ=255)
gAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaa < 1:2013282/70‑1 (MQ=255)
aaTCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaaaa > 1:2686764/1‑70 (MQ=255)
aaTCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAAc > 1:3882445/1‑71 (MQ=255)
aaTCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAAc > 1:1968815/1‑71 (MQ=255)
aTCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACt < 1:1375410/71‑1 (MQ=255)
aTCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACt < 1:502535/71‑1 (MQ=255)
aTCAACGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACt > 1:1632506/1‑71 (MQ=255)
tCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaa < 1:1529686/66‑1 (MQ=255)
aaCGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGa > 1:3933982/1‑70 (MQ=255)
aaCGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGa < 1:1730494/70‑1 (MQ=255)
aaCGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGa < 1:846882/70‑1 (MQ=255)
aCGGGAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGaaa < 1:3427792/71‑1 (MQ=255)
gggAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGt < 1:3461353/71‑1 (MQ=255)
gggAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGt < 1:1999788/71‑1 (MQ=255)
ggAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTg < 1:2865982/71‑1 (MQ=255)
ggAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTg < 1:3548431/71‑1 (MQ=255)
gAAACCTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTGa > 1:912822/1‑71 (MQ=255)
aaaCCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTGAc < 1:3065745/71‑1 (MQ=255)
aaCCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCg > 1:238910/1‑42 (MQ=255)
aaCCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaaaa < 1:1505293/59‑1 (MQ=255)
aaCCTTTTGGCCTCGATTACGAACTGGCGAAACAGTTTGCCg < 1:64172/42‑1 (MQ=255)
ccTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGAt < 1:826061/42‑1 (MQ=255)
ccTTTCGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGaaa > 1:611290/1‑63 (MQ=255)
ttGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTaaaa > 1:4096556/1‑53 (MQ=255)
ttGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTGACCGTGCgg > 1:1943680/1‑71 (MQ=255)
|
GAGAGTTGCGTGTGAGCACCATTCATACTCCCCTGACTTATAACGAAATCAACGGGAAACCTTTTGGCCTGGATTACGAACTGGCGAAACAGTTTGCCGATTACCTCGGCGTAAAACTGAAAGTGACCGTGCGG > minE/1728614‑1728747
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
