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 |
2,619,677 |
A→G |
57.9% |
Y354Y (TAT→TAC) |
zntA ← |
zinc, cobalt and lead efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,619,677 | 0 | A | G | 57.9%
| 20.5
/ 45.1
| 64 | Y354Y (TAT→TAC) | zntA | zinc, cobalt and lead efflux system |
| Reads supporting (aligned to +/- strand): ref base A (12/15); new base G (31/6); total (43/21) |
| Fisher's exact test for biased strand distribution p-value = 1.30e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01 |
TGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCT > minE/2619613‑2619734
|
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa > 1:19884/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa > 1:940490/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa > 1:846274/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa > 1:1174669/1‑69 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:2207471/69‑1 (MQ=255)
tGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:2211539/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:2815054/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:3213286/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:1607366/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:592156/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:135403/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:3202302/69‑1 (MQ=255)
gCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:1277104/69‑1 (MQ=255)
cACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATaa < 1:209127/68‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:1403107/69‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:3069154/69‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:2477753/69‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:1094997/69‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:2481791/69‑1 (MQ=255)
cAGCGTTACCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCg < 1:913888/69‑1 (MQ=255)
aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:3066179/43‑1 (MQ=255)
aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:1995341/43‑1 (MQ=255)
aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:153234/43‑1 (MQ=255)
aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:1396610/43‑1 (MQ=255)
aGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGa < 1:2458816/43‑1 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2763744/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2478615/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2358850/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2345198/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2321372/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:2181769/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:327510/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:1274166/3‑67 (MQ=255)
ttaCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTc > 1:1068341/3‑67 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCaa > 1:2386833/2‑68 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:3102736/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:378010/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:468730/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:2985705/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:2904186/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:534268/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:578750/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:71371/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:2562213/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:814914/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:240914/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:239925/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:2225678/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:22133/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:1747421/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:1559124/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:1379873/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:1324010/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:1142794/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGCTCAAt > 1:958432/2‑69 (MQ=255)
taCCAGCAGGGCGACGGCCATAATCGCTGGCGTGTAAATACGGCTGAAACGGTCGATAAACCGATCAAt > 1:981530/2‑69 (MQ=255)
aTCGCGGGCGTATAGATACTGCTGAAACGGTCGATAAACCGCTCAATGGCAg > 1:2145346/1‑52 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc > 1:3402567/1‑60 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc > 1:2592990/1‑60 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc > 1:1946408/1‑60 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc > 1:1066069/1‑60 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGct > 1:2494269/1‑69 (MQ=255)
aTCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGc > 1:1045715/1‑68 (MQ=255)
aTCGAGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGc > 1:2217670/1‑60 (MQ=255)
|
TGGCGGCAAACAGCAGCGGTGGCACCAGCGTCACCAGCAGAGCGACGGCCATAATCGCGGGCGTATAGATACGGCTGAAACGGTCGATAAACCGCTCAATGGGAGCGCGACGCTCTTCGGCT > minE/2619613‑2619734
|
| 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
