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 |
1,775,329 |
G→C |
34.5% |
G87G (GGG→GGC) |
yfiN → |
predicted diguanylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,775,329 | 0 | G | C | 34.5%
| 50.2
/ 41.3
| 55 | G87G (GGG→GGC) | yfiN | predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base G (14/22); new base C (12/7); total (26/29) |
| Fisher's exact test for biased strand distribution p-value = 9.92e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.12e-01 |
GTTTTTGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTGGCAT > minE/1775273‑1775386
|
gTTTTTGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAAc > 1:2987969/1‑68 (MQ=255)
gTTTTTGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAAc > 1:1194666/1‑68 (MQ=255)
gTTTTTGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAAc > 1:321426/1‑68 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:105301/68‑1 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:3278963/68‑1 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:3436429/68‑1 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:2010328/68‑1 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:1859098/68‑1 (MQ=255)
ttttGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:538795/68‑1 (MQ=255)
gATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTCAACTg < 1:3013929/61‑1 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:1547193/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:1777197/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:1469074/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:1381972/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:1987958/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:266698/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:2640643/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:2068004/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:919772/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:2524911/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:939188/1‑55 (MQ=255)
aTGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGCCAATTTTc > 1:227791/1‑55 (MQ=255)
cagcaACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAagc > 1:2908409/1‑69 (MQ=255)
cagcaACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAagc > 1:2970415/1‑69 (MQ=255)
cagcaACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAagc > 1:1998739/1‑69 (MQ=255)
cagcaACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGAGATAagc > 1:1627539/1‑69 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:1049358/38‑1 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:3175788/38‑1 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc > 1:2195408/1‑38 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:2460662/38‑1 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:3405032/38‑1 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:680466/38‑1 (MQ=255)
gAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:1469809/38‑1 (MQ=255)
aaaCACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTc < 1:947090/37‑1 (MQ=255)
cTGGCAGGGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:2680125/1‑68 (MQ=255)
cTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:280866/1‑68 (MQ=255)
cTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:2686186/1‑68 (MQ=255)
cTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:1352862/1‑68 (MQ=255)
cTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:3246049/1‑68 (MQ=255)
cTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCt > 1:3429565/1‑68 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:1312061/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:650348/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:1812286/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2073113/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2124425/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:3383991/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2224095/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2395066/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2398817/69‑1 (MQ=255)
cTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2430890/69‑1 (MQ=255)
tGGGCCAGCAAGGGCAATTTTGAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:2206705/68‑1 (MQ=255)
tGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTgg < 1:1379776/68‑1 (MQ=255)
ccAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTGGCAt < 1:468263/67‑1 (MQ=255)
ccAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTGGCAt < 1:1320398/67‑1 (MQ=255)
ccAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTGGCAt < 1:2706474/67‑1 (MQ=255)
|
GTTTTTGCCGATGGCCCTGCAGCAACTGAAACACTGGCAGCGCTGGGCCAGCAAGGGCAATTTTCAACTGCAGAAGTACGTGATAAGCAGCAAAATATTCTGGCATCCTGGCAT > minE/1775273‑1775386
|
| 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
