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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,614,173 |
T→A |
44.9% |
P16P (CCA→CCT) |
acpT ← |
holo‑(acyl carrier protein) synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,614,173 | 0 | T | A | 44.9%
| 9.3
/ 51.6
| 49 | P16P (CCA→CCT) | acpT | holo‑(acyl carrier protein) synthase 2 |
| Reads supporting (aligned to +/- strand): ref base T (9/18); new base A (5/17); total (14/35) |
| Fisher's exact test for biased strand distribution p-value = 5.30e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
AGCCAGCGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGTT > minE/2614117‑2614235
|
agccagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTgcgc > 1:2954287/1‑67 (MQ=255)
agccagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCtt < 1:583363/69‑1 (MQ=255)
agccagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCtt < 1:1983862/69‑1 (MQ=255)
agccagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCtt < 1:1875297/69‑1 (MQ=255)
gccagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCtt < 1:2877971/68‑1 (MQ=255)
cagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAg < 1:2706233/69‑1 (MQ=255)
cagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAg < 1:465514/69‑1 (MQ=255)
cagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAg < 1:1317577/69‑1 (MQ=255)
cagcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAg < 1:1638795/69‑1 (MQ=255)
gcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAgg > 1:1010191/1‑68 (MQ=255)
gcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAgg > 1:2466171/1‑68 (MQ=255)
gcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAgg > 1:2155192/1‑68 (MQ=255)
gcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAgg > 1:3281841/1‑68 (MQ=255)
gcGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAgg > 1:384660/1‑68 (MQ=255)
tCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGaa < 1:1556868/69‑1 (MQ=255)
tCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGaa < 1:435314/69‑1 (MQ=255)
aCCTTGCGGTGCTTGCTCGCGTAAACCCGGTGTCAGAGGAGCTGCGCTTAAGGTCGAAACt > 1:1729889/1‑61 (MQ=255)
aCCTTGCGGTGCTTGCTCGCGTAAACCCGGTGTCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAg > 1:1506589/1‑69 (MQ=255)
aCCTTGCGGTGCTTGCTCGCGTAAACCCGGTGTCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAg > 1:2995837/1‑69 (MQ=255)
aCCTTGCGGTGCTTGCTCGCGTAAACCCGGTGTCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAg > 1:1079680/1‑69 (MQ=255)
aCCTTGCGGTGCTTGCTCGCGTAAACCCGGTGTCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAg > 1:2471299/1‑69 (MQ=255)
tGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACt > 1:2698872/1‑69 (MQ=255)
tGCGGTGCTTGCTCGCGTAAAACCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACt > 1:2310567/1‑69 (MQ=255)
gTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATcc < 1:3154167/69‑1 (MQ=255)
gTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATcc < 1:2398280/69‑1 (MQ=255)
gTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATcc < 1:2476809/69‑1 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa > 1:387409/1‑68 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa < 1:512982/68‑1 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa < 1:1038753/68‑1 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa < 1:1042624/68‑1 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa < 1:1044229/68‑1 (MQ=255)
tgctCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATa < 1:117118/68‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:884017/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:2772470/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:83499/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:825482/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:636985/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:1061161/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:1154100/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:1524513/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:3293310/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:1678982/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:3167518/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:2033972/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:2142795/69‑1 (MQ=255)
tGGCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:2330691/69‑1 (MQ=255)
ggCAGAGGAGCTGCGGTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:3086485/68‑1 (MQ=255)
ggCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:495065/68‑1 (MQ=255)
ggCAGAGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGtt < 1:1884558/68‑1 (MQ=255)
|
AGCCAGCGTTCGCGTCGTGGACCTTGCGGTGCTTGCTCGCGTAAACCCGGTGGCAGTGGAGCTGCGCTTAAGGTCGAAACTTTCCCCAGAACTATCCGATACATATCAGGGCCAACGTT > minE/2614117‑2614235
|
| 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
