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 F28 I3 R2
|
122 |
64.1 |
3058059 |
97.6% |
2984665 |
63.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
1,439,412 |
G→A |
A297V (GCT→GTT) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,439,412 | 0 | G | A | 98.0%
| 139.4
/ ‑3.8
| 49 | A297V (GCT→GTT) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base A (27/21); total (28/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
CATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTT > minE/1439347‑1439479
|
catATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAAGCAgg > 1:628188/1‑71 (MQ=255)
catATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAgg > 1:1518028/1‑71 (MQ=255)
atatTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAggg < 1:2978304/71‑1 (MQ=255)
tatTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGgga > 1:2591285/1‑71 (MQ=255)
tttCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGggacg > 1:595507/1‑71 (MQ=255)
tttCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGggac < 1:2949977/70‑1 (MQ=255)
ttCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGggacg < 1:2876370/70‑1 (MQ=255)
ttCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGggacg > 1:1740517/1‑70 (MQ=255)
tCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGAcc > 1:2698284/1‑71 (MQ=255)
cgtcgtcgtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGaa < 1:1058503/70‑1 (MQ=255)
cgtcgtcgtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGaa < 1:2874952/70‑1 (MQ=255)
cgtcgtcgtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAg > 1:2768243/1‑71 (MQ=255)
gtcgtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCa > 1:2475644/1‑47 (MQ=255)
gtcgtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCg < 1:567221/70‑1 (MQ=255)
gtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGaa > 1:2063022/1‑63 (MQ=255)
gtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAAc < 1:730256/70‑1 (MQ=255)
gtAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACt > 1:2486891/1‑71 (MQ=255)
tAGCCACGACCCAGGTTTTTACCTTTAGACTGCGGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTg > 1:995488/1‑71 (MQ=255)
ccACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTa > 1:521612/1‑71 (MQ=255)
aCGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAg < 1:222993/58‑1 (MQ=255)
aCGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:2621431/71‑1 (MQ=255)
cGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt > 1:737793/1‑70 (MQ=255)
cGACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt > 1:2206326/1‑70 (MQ=255)
gACCCAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt > 1:8592/1‑69 (MQ=255)
cccAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGc < 1:1451835/71‑1 (MQ=255)
cccAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGc < 1:1256761/71‑1 (MQ=255)
ccAGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGa < 1:3002875/68‑1 (MQ=255)
aGGTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGAGGCAGACCGAAGTCGAACTGGTACTGAGCAAc < 1:1541436/71‑1 (MQ=255)
gTTTTTACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGa < 1:1838022/64‑1 (MQ=255)
ttttACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCt > 1:231201/1‑71 (MQ=255)
tttACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCtt > 1:721988/1‑71 (MQ=255)
ttACCTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTc > 1:2928643/1‑71 (MQ=255)
cTTTAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACt < 1:1277669/54‑1 (MQ=255)
ttAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGtt > 1:786308/1‑71 (MQ=255)
tAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTa > 1:2083913/1‑49 (MQ=255)
tAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCt > 1:306525/1‑62 (MQ=255)
tAGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTc > 1:2013988/1‑71 (MQ=255)
aGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTg > 1:1979314/1‑45 (MQ=255)
aGACTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTc < 1:2280021/70‑1 (MQ=255)
aCTGCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCtg < 1:1011433/70‑1 (MQ=255)
gCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAAc > 1:1818440/1‑38 (MQ=255)
gCAGGTAAACCAGGGACGGACGCAGACCGAAGTCGAAc > 1:2247296/1‑38 (MQ=255)
aGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCtgt > 1:2570995/1‑66 (MQ=255)
aGGTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCttt < 1:1745103/71‑1 (MQ=255)
ggTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTg < 1:1396778/71‑1 (MQ=255)
ggTAAACCAGGGACGGACGAAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCttt > 1:981714/1‑70 (MQ=255)
gTAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACa < 1:3048001/49‑1 (MQ=255)
tAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACa < 1:2811679/48‑1 (MQ=255)
tAAACCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGtt > 1:407747/1‑71 (MQ=255)
|
CATATTTCAGGATATCTTCGTCGTCGTAGCCACGACCCAGGTTTTTACCTTTAGACTGCAGGTAAGCCAGGGACGGACGCAGACCGAAGTCGAACTGGTACTGAGCAACAGCTTCGAAGTTCTGTGCTTTGTT > minE/1439347‑1439479
|
| 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
