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 |
2,698,806 |
G→T |
41.5% |
V154V (GTG→GTT) |
yrfD → |
predicted pilus assembly protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,698,806 | 0 | G | T | 41.5%
| 50.3
/ 66.1
| 77 | V154V (GTG→GTT) | yrfD | predicted pilus assembly protein |
| Reads supporting (aligned to +/- strand): ref base G (22/23); new base T (7/25); total (29/48) |
| Fisher's exact test for biased strand distribution p-value = 1.86e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
TGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCTCAT > minE/2698739‑2698866
|
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCAtgtg > 1:1597271/1‑68 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:2475998/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:3152931/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:2059996/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:1281139/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:1327906/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:1413222/1‑69 (MQ=255)
tGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGa > 1:3030615/1‑69 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:3052061/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:3151902/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:3316003/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:2905928/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:456264/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:613099/69‑1 (MQ=255)
gCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGcgcg < 1:2354012/69‑1 (MQ=255)
gcgcAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGAt < 1:282267/68‑1 (MQ=255)
gcgcAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGAt < 1:2201354/68‑1 (MQ=255)
gcgcAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGAt < 1:1272676/68‑1 (MQ=255)
gcgcAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGAt < 1:1146864/68‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCTCGATCACTCCg < 1:3433841/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:359550/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:2740688/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:839300/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:1034304/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:261942/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:800606/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:2552989/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:76523/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:2553253/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:97070/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:1556520/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:1553854/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:2048863/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:1218242/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:891560/69‑1 (MQ=255)
agcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:1704821/69‑1 (MQ=255)
gcaaagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCg < 1:2500028/68‑1 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:1848281/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:1458107/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:164999/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:1702695/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:332945/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:666019/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTTAGCGCGATCACTCCGGAt > 1:2242033/1‑68 (MQ=255)
aagAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGAt > 1:1726318/1‑68 (MQ=255)
tGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTg < 1:1431580/69‑1 (MQ=255)
tGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTg < 1:2492286/69‑1 (MQ=255)
tGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTg < 1:3125911/69‑1 (MQ=255)
tGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTg < 1:3348213/69‑1 (MQ=255)
tACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:2889955/68‑1 (MQ=255)
tACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:514176/68‑1 (MQ=255)
tACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:2894060/68‑1 (MQ=255)
tACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:2572969/68‑1 (MQ=255)
aaGGTTTCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCtttttt > 1:437527/1‑69 (MQ=255)
aaGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCg > 1:3214137/1‑54 (MQ=255)
aaGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCtttttt > 1:2199150/1‑69 (MQ=255)
aaGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCtttttt > 1:45330/1‑69 (MQ=255)
aaGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCttttt > 1:1482123/1‑68 (MQ=255)
aaGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCttttt > 1:3013572/1‑68 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:785128/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:1081980/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:629000/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:997776/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:1155996/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:2648238/1‑40 (MQ=255)
tGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:2154832/1‑40 (MQ=255)
ggCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGc > 1:3144612/2‑40 (MQ=255)
tgtTCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCtca < 1:738026/69‑1 (MQ=255)
tgtTCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCtca < 1:2163700/69‑1 (MQ=255)
ttCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTTCAGCGATTCCTGCCTTTTTTACCTTCtcat < 1:3428871/68‑1 (MQ=255)
ttCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCtcat < 1:2673897/68‑1 (MQ=255)
ttCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCtcat < 1:2003802/68‑1 (MQ=255)
ttCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCtcat < 1:1042199/68‑1 (MQ=255)
ttCATGTTAGCGCGATCACTCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCCTCtcat < 1:434865/68‑1 (MQ=255)
cATGTGAGCGCGATCACCCCGGATGGCAGTGCATTACAGCGAt < 1:2723869/43‑1 (MQ=255)
cATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:517946/43‑1 (MQ=255)
cATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:800973/43‑1 (MQ=255)
cATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGAt < 1:165558/43‑1 (MQ=255)
|
TGACTGCCGCGCAAAGCAAAGAGCTGGCAACGCTGCTTACTCTGGCAGAAAGGTTGCGTGTTCATGTGAGCGCGATCACCCCGGATGCCAGTGCATTACAGCGATTCCTGCCTTTTTTACCTTCTCAT > minE/2698739‑2698866
|
| 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
