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 |
2,861,639 |
C→T |
67.5% |
D242D (GAC→GAT) |
miaA → |
delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,861,639 | 0 | C | T | 67.5%
| 33.4
/ 21.4
| 46 | D242D (GAC→GAT) | miaA | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase |
| Reads supporting (aligned to +/- strand): ref base C (11/4); new base T (6/25); total (17/29) |
| Fisher's exact test for biased strand distribution p-value = 7.72e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CAGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCAT > minE/2861571‑2861703
|
caGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGTGATTTGCATACGGAc > 1:1381095/1‑69 (MQ=255)
caGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGAc > 1:998288/1‑69 (MQ=255)
caGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGAc > 1:864956/1‑69 (MQ=255)
caGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGAc > 1:1682742/1‑69 (MQ=255)
aGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGAc > 1:3123685/1‑68 (MQ=255)
aGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGAc > 1:1385479/1‑68 (MQ=255)
aGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACt > 1:1099077/1‑69 (MQ=255)
aGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACt > 1:2070865/1‑69 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:3140792/1‑68 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:3392963/1‑68 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:1311669/1‑68 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:1431880/1‑68 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:2496642/1‑68 (MQ=255)
tGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGATTTGCCt > 1:1686373/1‑68 (MQ=255)
ggCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTc > 1:1744621/1‑69 (MQ=255)
ggCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTc > 1:51619/1‑69 (MQ=255)
gTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGtt > 1:296138/1‑69 (MQ=255)
gTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGtt > 1:2636538/1‑69 (MQ=255)
gTTTTGAAGCAGAAGTCCGGGCGCTTTTTGACCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGtt > 1:1704340/1‑69 (MQ=255)
gCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGt < 1:201451/69‑1 (MQ=255)
cGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTc < 1:1204336/44‑1 (MQ=255)
ccGAGGAGATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:2525482/68‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:3203546/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:2860780/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:940079/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:3208598/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:913175/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:857334/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:361001/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:477097/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:754561/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:595809/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:530566/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:1666493/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:1113813/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:120484/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:1283636/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:1445945/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:1543284/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:2111859/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:2881742/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:292347/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:3152928/66‑1 (MQ=255)
gaggagATTTGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCCCCAGATGTGGTCTTAcc < 1:973944/66‑1 (MQ=255)
tttGCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:2541231/59‑1 (MQ=255)
tttGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTTAAGGCGa < 1:1381218/69‑1 (MQ=255)
tttGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGa < 1:3196089/69‑1 (MQ=255)
gCATACGGATTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTAcc < 1:843169/56‑1 (MQ=255)
cGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCAt > 1:2002845/1‑69 (MQ=255)
cGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCAt > 1:622946/1‑69 (MQ=255)
cGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCAt > 1:2685092/1‑69 (MQ=255)
cGGACTAGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCa > 1:4443/1‑68 (MQ=255)
|
CAGATGTTGGCTTCAGGTTTTGAAGCAGAAGTCCGGGCGCTTTTTGCCCGAGGAGATTTGCATACGGACTTGCCTTCCATTCGTTGCGTGGGTTATCGCCAGATGTGGTCTTACCTTGAAGGCGAAATCTCAT > minE/2861571‑2861703
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
