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 |
1,859,000 |
G→A |
56.9% |
D194D (GAC→GAT) |
cysI ← |
sulfite reductase, beta subunit, NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,859,000 | 0 | G | A | 56.9%
| 11.5
/ 43.4
| 58 | D194D (GAC→GAT) | cysI | sulfite reductase, beta subunit, NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base G (16/9); new base A (20/13); total (36/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.90e-01 |
TTACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAACAGATGCTCAGAAATCTTC > minE/1858938‑1859057
|
ttACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGc < 1:2430321/69‑1 (MQ=255)
ttACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGc < 1:1000777/69‑1 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:2138611/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:1077334/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:216/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:878851/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:3132974/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:1668437/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:1335194/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:2484308/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:3323032/1‑66 (MQ=255)
tACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGa > 1:1475623/1‑66 (MQ=255)
gcgGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAg < 1:893797/68‑1 (MQ=255)
gcgGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAg < 1:627454/68‑1 (MQ=255)
gcgGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAg < 1:810560/68‑1 (MQ=255)
ggtaggtCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg < 1:1373355/69‑1 (MQ=255)
ggtaggtCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg < 1:1082495/69‑1 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:2675467/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:251239/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:3296194/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:2772658/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:339141/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:3409409/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:2840085/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:206001/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:205843/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:352295/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:478113/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:487088/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:490950/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:1513859/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:1480459/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:1432525/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:1255127/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:710009/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:1197909/1‑68 (MQ=255)
aGGATCGGCTCTTCATCAGTAGTGGCGACTCTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGt > 1:3134343/1‑68 (MQ=255)
cttcATCAGTCGTGGCGACTTTTTCCTGGTCGAGCCAg < 1:2795680/38‑1 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:347268/1‑43 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:2431418/1‑43 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:2753783/1‑43 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:1140171/1‑43 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:2164907/1‑43 (MQ=255)
tcatcaGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCg > 1:1872769/1‑43 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:2733011/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1168037/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1246826/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1345519/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1667545/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1783823/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:373171/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1907681/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:1918017/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:340252/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:2318327/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:2620612/68‑3 (MQ=255)
gACTTTTTCCTGATCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAGCAGATGTTCAGAAAttt < 1:2691972/68‑3 (MQ=255)
aCTTTTTCCTGGTCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAACAGATGCTCAGAAAtcttc < 1:1054786/69‑1 (MQ=255)
|
TTACGCGGCAGGTAGGTCTGGCCGAGGATCGGTTCTTCATCAGTAGTGGCGACTTTTTCCTGGTCGAGCCAGATCTCCGCATACGCGCGGGTACGAGGCAACAGATGCTCAGAAATCTTC > minE/1858938‑1859057
|
| 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
