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 |
|
A75 F1 I1 R1
|
16 |
50.8 |
3316832 |
95.7% |
3174208 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,972 |
G→A |
D37N (GAT→AAT) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,972 | 0 | G | A | 95.9%
| 181.0
/ ‑0.4
| 49 | D37N (GAT→AAT) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (27/20); total (28/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.18e-01 |
TGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAT > REL606/3145899‑3146046
|
tGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAAt > 1:888474/1‑76 (MQ=255)
gTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAAtt > 1:704472/1‑76 (MQ=255)
aaGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCg > 2:161656/1‑76 (MQ=255)
aGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGa < 1:317635/76‑1 (MQ=255)
gAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAg < 1:237748/76‑1 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcat > 1:765971/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcat > 1:1415424/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcat > 1:1449552/1‑76 (MQ=255)
aaGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcat > 1:310638/1‑76 (MQ=255)
aGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcatc < 1:1337490/76‑1 (MQ=255)
gCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGAcatcat > 1:1648166/1‑76 (MQ=255)
cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACatcatc > 2:137060/1‑76 (MQ=255)
cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACatcatc > 2:1431880/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCa > 2:1172134/1‑76 (MQ=255)
aTCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCa < 1:1109370/76‑1 (MQ=255)
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCaa < 1:353563/76‑1 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATg > 2:1252150/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATg > 2:148237/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATg > 2:687137/1‑76 (MQ=255)
aCCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGCTTCAGATCAGATCGAAGACATCATCCAAATGa > 2:96539/1‑76 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGAt > 1:796175/1‑76 (MQ=255)
tGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAAc > 2:63290/1‑76 (MQ=255)
cGAGGTCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGAc < 1:952572/76‑1 (MQ=255)
tCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATggg > 1:746387/1‑76 (MQ=255)
tCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATggg < 1:1025636/76‑1 (MQ=255)
tCAATGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATggg < 1:1239840/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCa < 2:948070/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCa > 2:1446569/1‑76 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCa > 2:132948/1‑76 (MQ=255)
aTGACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCAt > 2:48652/1‑76 (MQ=255)
gACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTc < 1:1606571/76‑1 (MQ=255)
gACCATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTc < 2:917072/76‑1 (MQ=255)
cATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAgg > 2:1161884/1‑76 (MQ=255)
cATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAgg > 2:586071/1‑76 (MQ=255)
cATCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAgg > 2:1326520/1‑76 (MQ=255)
cATCTGCCGGAAGATATCCTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAgg > 2:672174/1‑76 (MQ=255)
aTCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGt > 2:605829/1‑76 (MQ=255)
tCTGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTg < 2:23/76‑1 (MQ=255)
tGCCGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGAt < 1:1106174/76‑1 (MQ=255)
ccGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATgg < 1:1066331/76‑1 (MQ=255)
cGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga < 1:1596510/76‑1 (MQ=255)
cGGAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGga < 1:829826/76‑1 (MQ=255)
ggAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa > 1:185451/1‑76 (MQ=255)
ggAAGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaa < 1:760337/76‑1 (MQ=255)
aaGATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga < 2:1094064/76‑1 (MQ=255)
gATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag < 1:457787/76‑1 (MQ=255)
gATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag < 1:1086418/76‑1 (MQ=255)
gATATCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag < 1:462045/76‑1 (MQ=255)
tatCGTCAATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCa > 2:1410276/1‑76 (MQ=255)
cgtcaATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg > 2:1293821/1‑76 (MQ=255)
cgtcaATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg > 2:1214660/1‑76 (MQ=255)
cgtcaATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg > 1:30318/1‑76 (MQ=255)
cgtcaATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg > 2:616262/1‑76 (MQ=255)
gtcgATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCgg < 1:251279/76‑1 (MQ=255)
cgATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt < 2:194729/76‑1 (MQ=255)
cgATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt < 2:1048463/76‑1 (MQ=255)
|
TGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAT > REL606/3145899‑3146046
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
