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 |
|
A139 F1 I1 R1
|
15 |
48.9 |
3081653 |
97.3% |
2998448 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,162,470 |
A→C |
T539P (ACC→CCC) |
rpoB → |
DNA‑directed RNA polymerase subunit beta |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,162,470 | 0 | A | C | 97.6%
| 165.0
/ ‑4.0
| 41 | T539P (ACC→CCC) | rpoB | DNA‑directed RNA polymerase subunit beta |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (20/20); total (20/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01 |
ATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCG > REL606/4162398‑4162539
|
aTGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGcccc > 1:1462001/1‑76 (MQ=255)
tGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCg > 2:1390191/1‑76 (MQ=255)
ccAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGaa < 1:46967/76‑1 (MQ=255)
cAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAAc > 1:897898/1‑76 (MQ=255)
aacaacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCTGCCCAGGCGGTCTGCCCCGTGAACGTg < 2:887288/76‑1 (MQ=255)
aacaacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTg < 1:1118017/76‑1 (MQ=255)
accccGCGGTGTGAGAGTACGCACAAGCGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAg < 2:150282/74‑1 (MQ=255)
aacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAg > 2:264725/1‑76 (MQ=255)
aacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAg > 1:1059559/1‑76 (MQ=255)
acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAgg < 2:374901/76‑1 (MQ=255)
acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAgg < 1:400746/76‑1 (MQ=255)
acCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAgg < 1:526155/76‑1 (MQ=255)
cccGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGc > 2:90169/1‑76 (MQ=255)
gCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTc < 1:721815/76‑1 (MQ=255)
tGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGa < 1:109740/76‑1 (MQ=255)
tGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGa > 1:729367/1‑76 (MQ=255)
gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa > 2:1487328/1‑76 (MQ=255)
tCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAg < 1:1301011/76‑1 (MQ=255)
cTGAGATTACGCACAAACGTCGTATCTCCGCAGTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGt < 1:581737/76‑1 (MQ=255)
aTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCgag > 2:1119491/1‑76 (MQ=255)
aTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCgag < 1:1326337/76‑1 (MQ=255)
tACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGAc < 2:842415/76‑1 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACg < 1:33469/76‑1 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACg > 1:235125/1‑76 (MQ=255)
gCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTa < 1:428811/76‑1 (MQ=255)
gCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTa < 1:208919/76‑1 (MQ=255)
cacaAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTac > 1:517055/1‑76 (MQ=255)
caAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTacac > 2:1401496/1‑76 (MQ=255)
aaCGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACAccc < 2:480584/76‑1 (MQ=255)
cgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTc < 1:450709/76‑1 (MQ=255)
cgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTc > 1:1308098/1‑76 (MQ=255)
cgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTc > 2:62534/1‑76 (MQ=255)
gtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCa > 2:978925/1‑76 (MQ=255)
tATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCAc > 2:500361/1‑76 (MQ=255)
tATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCAc > 2:902865/1‑76 (MQ=255)
ctcCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACAACCGACTCACTAc > 1:516502/1‑76 (MQ=255)
cccGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACg < 1:1429339/75‑1 (MQ=255)
cACTCGGCCCAGTCGGGCTGCCCCCCAAACGAGCAGGCTTCGAAGCTCGAGACGCCCACCCCACTCACTACGGTcg > 2:615970/1‑76 (MQ=255)
gCCCGGTCGGTCTGCCCGGTTGGCGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATg < 2:465039/76‑1 (MQ=255)
cAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTcc < 1:1013417/76‑1 (MQ=255)
ggCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCaa > 2:642550/1‑76 (MQ=255)
ggCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCaa > 1:343843/1‑76 (MQ=255)
gCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAAt < 1:1271051/76‑1 (MQ=255)
cGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACTCCCGACTCACTACGGTCGCGTATGTCCAATc < 1:214276/76‑1 (MQ=255)
ggTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCg > 2:148567/1‑76 (MQ=255)
|
ATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCG > REL606/4162398‑4162539
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
