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 |
|
A89 F1 I1 R1
|
15 |
55.0 |
3646496 |
95.5% |
3482403 |
75.9 |
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 | 94.7%
| 141.7
/ ‑3.2
| 38 | T539P (ACC→CCC) | rpoB | DNA‑directed RNA polymerase subunit beta |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base C (25/11); total (26/12) |
| Fisher's exact test for biased strand distribution p-value = 5.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
TATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAA > REL606/4162397‑4162542
|
tATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGccc < 1:1428868/76‑1 (MQ=255)
tGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCg < 2:496375/76‑1 (MQ=255)
ggACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGt > 1:71950/1‑76 (MQ=255)
aGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGGACg > 1:1166000/1‑76 (MQ=255)
gAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCACCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGt < 2:1652776/76‑1 (MQ=255)
aacaacCCGCTGTCTGAGATTACGCACAAACGTCGTATCCTCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTg < 2:1651210/76‑1 (MQ=255)
acaacCCTCTGTCTGAGAATACGCACAAACGTCATATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGc < 2:1164173/76‑1 (MQ=255)
naacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCa > 1:1691799/2‑76 (MQ=255)
caacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCa > 1:431642/1‑76 (MQ=255)
aacCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGACCGTGCAg > 2:1247125/1‑76 (MQ=255)
cccGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGc > 2:34646/1‑76 (MQ=255)
ccGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCt > 2:449538/1‑76 (MQ=255)
cGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCtt > 2:207409/1‑76 (MQ=255)
cGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCtt < 1:150060/76‑1 (MQ=255)
gCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTc > 1:96606/1‑76 (MQ=255)
cTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCg > 1:1422771/1‑76 (MQ=255)
gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa > 2:1440245/1‑76 (MQ=255)
gTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGaa > 2:523385/1‑76 (MQ=255)
tCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGGGCAGGGTTCGacg > 1:911540/1‑74 (MQ=255)
tGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGtt < 1:805636/76‑1 (MQ=255)
gagaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTc > 2:111225/1‑76 (MQ=255)
gagaTTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTc > 1:645334/1‑76 (MQ=255)
ttACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCgaga < 1:779736/76‑1 (MQ=255)
ttACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGGCTGCGCCGTGAGAGATCAAGCTTAGAAGATCgaga > 2:1025206/1‑76 (MQ=255)
aCGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACg > 2:557230/1‑76 (MQ=255)
gCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTa < 1:656334/76‑1 (MQ=255)
cgtcgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGa > 2:916373/1‑76 (MQ=255)
gtcgtATCTCCGCACTCGGCCCAGGCTGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGAc > 1:146753/1‑76 (MQ=255)
tcgtATCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACt > 1:427178/1‑76 (MQ=255)
aTCTCCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACt > 2:1036994/1‑76 (MQ=255)
tcCGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACg > 2:1521908/1‑76 (MQ=255)
ccGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTAcag > 2:1283379/1‑74 (MQ=255)
ccGCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACgg > 1:584965/1‑76 (MQ=255)
gCACTCGGCCCAGGGGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTc < 1:448260/76‑1 (MQ=255)
gCACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTc > 2:979246/1‑76 (MQ=255)
cACTCGGCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTcg < 2:1239043/76‑1 (MQ=255)
cGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTa < 2:1197538/76‑1 (MQ=255)
ggCCCAGGCGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTAt > 2:1300691/1‑76 (MQ=255)
cGGTCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc > 1:1629399/1‑76 (MQ=255)
cGGTCTGCCCCGTGAACGTGCAGCCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATc > 1:941961/1‑76 (MQ=255)
ggTCTGACCCGTGAACGTACAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCg < 2:75205/76‑1 (MQ=255)
tCTGCCCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaa < 2:431642/76‑1 (MQ=255)
cTGCCCCGTGAACGTGCAGGCTTCGAAGATCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaaa > 1:1428693/1‑76 (MQ=255)
cTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGaaa > 2:1770415/1‑76 (MQ=255)
|
TATGGACCAGAACAACCCGCTGTCTGAGATTACGCACAAACGTCGTATCTCCGCACTCGGCCCAGGCGGTCTGACCCGTGAACGTGCAGGCTTCGAAGTTCGAGACGTACACCCGACTCACTACGGTCGCGTATGTCCAATCGAAA > REL606/4162397‑4162542
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
