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 |
1,050,725 |
T→C |
25.4% |
V305A (GTC→GCC) |
ydhK → |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,050,725 | 0 | T | C | 25.4%
| 84.7
/ 33.0
| 55 | V305A (GTC→GCC) | ydhK | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base T (23/18); new base C (9/5); total (32/23) |
| Fisher's exact test for biased strand distribution p-value = 7.56e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.66e-01 |
GCGCTCGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCTGCAAAG > minE/1050655‑1050791
|
gcgcTCGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGt < 1:1934015/71‑1 (MQ=255)
gcTCGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCg < 1:3613487/71‑1 (MQ=255)
cGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGcc > 1:669165/1‑70 (MQ=255)
cGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGcc > 1:35200/1‑70 (MQ=255)
gCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGcc < 1:966899/69‑1 (MQ=255)
gCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGa > 1:3657242/1‑71 (MQ=255)
cAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACt < 1:2295473/71‑1 (MQ=255)
tCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTc > 1:1301653/1‑60 (MQ=255)
cGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCg < 1:1545687/70‑1 (MQ=255)
gCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCg < 1:2543752/69‑1 (MQ=255)
cAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGc < 1:314439/70‑1 (MQ=255)
gATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGc > 1:3769046/1‑71 (MQ=255)
aTGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGcc < 1:1590/71‑1 (MQ=255)
tGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTAt < 1:3631222/58‑1 (MQ=255)
tACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCCACGCCGCCGACTATCGGCACGTCGCCATCTg > 1:3153151/1‑71 (MQ=255)
tACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCt < 1:2577585/70‑1 (MQ=255)
cacCGTCGCACGTATTATCTCCCCGCTACGCCCGACCAACGTCGCCGa > 1:1098086/1‑48 (MQ=255)
cacCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGa > 1:2373453/1‑48 (MQ=255)
cacCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGa > 1:3901018/1‑48 (MQ=255)
cacCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTgg > 1:1511297/1‑70 (MQ=255)
cacCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGc < 1:3015222/71‑1 (MQ=255)
acCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTgg > 1:3847414/1‑69 (MQ=255)
acCGTCGCACGTATTATCGCACCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTgg > 1:1222515/1‑69 (MQ=255)
cGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGc > 1:204310/1‑71 (MQ=255)
cGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGc > 1:3927350/1‑71 (MQ=255)
cGTATTATCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCa > 1:2327369/1‑47 (MQ=255)
gTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGt > 1:546837/1‑71 (MQ=255)
gTATTATCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCACg < 1:2339223/48‑1 (MQ=255)
ttatCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAt > 1:2109643/1‑71 (MQ=255)
tatCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAtt > 1:3793627/1‑71 (MQ=255)
atCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCa > 1:752516/1‑41 (MQ=255)
atCGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAt > 1:667774/1‑69 (MQ=255)
tCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGtt > 1:3422114/1‑66 (MQ=255)
tCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAtttt < 1:1639329/71‑1 (MQ=255)
tCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAttt < 1:218174/70‑1 (MQ=255)
cGCCCCGCTACGCCCGACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGAc < 1:3675040/59‑1 (MQ=255)
gCCCCGCTACGCCCGACCAACGCCGCCGACTATCg > 1:3905158/1‑35 (MQ=255)
cccGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAttt < 1:115593/66‑1 (MQ=255)
cccGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAttt < 1:2512878/66‑1 (MQ=255)
gCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTgccgcc > 1:2960372/1‑71 (MQ=255)
cTACGCCCGTCCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTgccgcc < 1:663104/70‑1 (MQ=255)
cTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCt < 1:1578871/71‑1 (MQ=255)
cGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTg < 1:594681/41‑1 (MQ=255)
cGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTa < 1:693911/71‑1 (MQ=255)
gCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTAt < 1:3862868/71‑1 (MQ=255)
gCCCGACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTAt < 1:3837095/71‑1 (MQ=255)
cccGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATc > 1:19045/1‑71 (MQ=255)
ccGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTAttttt > 1:3045232/1‑58 (MQ=255)
ccGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCt > 1:1230414/1‑71 (MQ=255)
gACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATc > 1:80136/1‑68 (MQ=255)
gACCAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGACTTTATCTg > 1:1199802/1‑70 (MQ=255)
ccAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCTGCa > 1:60516/1‑70 (MQ=255)
cAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGc > 1:738973/1‑38 (MQ=255)
cAACGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCTGCa > 1:2202251/1‑69 (MQ=255)
aaCGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCTGCAAag > 1:703253/1‑71 (MQ=255)
aCGCCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTgc < 1:3585058/53‑1 (MQ=255)
|
GCGCTCGCCAGTTCGCAAACAGATGTTTACACCGTCGCACGTATTATCGCCCCGCTACGCCCGACCAACGTCGCCGACTATCGGCACGTCGCCTTCTGGCAGCGACTACGTTATTTTTGCCGCCTTTATCTGCAAAG > minE/1050655‑1050791
|
| 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
