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 |
|
A41 F1 I1 R1
|
21 |
57.1 |
3643130 |
97.0% |
3533836 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,985 |
T→G |
I41S (ATC→AGC) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,985 | 0 | T | G | 97.8%
| 194.4
/ ‑4.2
| 46 | I41S (ATC→AGC) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (18/27); total (18/28) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
AAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGA > REL606/3145912‑3146054
|
aaGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGACGATATCGTCGATTCAGATCAGAGCg > 2:1480915/1‑76 (MQ=255)
aaGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCg > 1:1103286/1‑76 (MQ=255)
aaGGAGCAAGGCTAGCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCg < 2:538410/76‑1 (MQ=255)
aGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGa < 1:1239065/76‑1 (MQ=255)
ggAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGaa < 1:802947/76‑1 (MQ=255)
ggAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGaa < 1:1346199/76‑1 (MQ=255)
gAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATANTCGATTCAGATCAGAGCGAAg > 2:295839/1‑76 (MQ=255)
aGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGAcatc < 1:1048037/76‑1 (MQ=255)
cTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACatcatc > 1:1785651/1‑76 (MQ=255)
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCaa > 2:1367034/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATg > 2:1772038/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATg < 1:1580026/76‑1 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATg < 1:577297/76‑1 (MQ=255)
aCCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGa < 2:1147071/76‑1 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGAt < 2:1175545/76‑1 (MQ=255)
cTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATc > 1:1059005/1‑76 (MQ=255)
tATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCa < 1:928947/76‑1 (MQ=255)
aTGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCaa < 1:971983/76‑1 (MQ=255)
aTGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCaa < 1:604795/76‑1 (MQ=255)
aTGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCaa < 1:1044005/76‑1 (MQ=255)
tGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAAc > 1:428678/1‑76 (MQ=255)
gCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACg < 1:1268689/76‑1 (MQ=255)
ggTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATg < 2:57961/76‑1 (MQ=255)
gTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATgg < 1:907669/76‑1 (MQ=255)
gTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATgg > 1:882130/1‑76 (MQ=255)
gTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATgg < 2:1439043/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCa > 1:1428902/1‑76 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCa > 1:1816771/1‑76 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCa < 1:738597/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCa < 1:621923/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCa < 1:20695/76‑1 (MQ=255)
aTGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCAt > 1:306466/1‑76 (MQ=255)
tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCAtt < 2:1205591/76‑1 (MQ=255)
tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCAtt < 1:135083/76‑1 (MQ=255)
tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCAtt < 2:1741846/76‑1 (MQ=255)
aTCTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGt < 2:503319/76‑1 (MQ=255)
cTGCCGGAAGATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGa > 1:523424/1‑76 (MQ=255)
gATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag > 1:570915/1‑76 (MQ=255)
gATATCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGaagaag < 1:1362961/76‑1 (MQ=255)
tatCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCa > 2:1133158/1‑76 (MQ=255)
tatCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCa < 1:1479132/76‑1 (MQ=255)
atCGTCGATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc > 2:1394846/1‑76 (MQ=255)
gATTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATg < 2:1312170/76‑1 (MQ=255)
aTTCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGc < 2:1731634/76‑1 (MQ=255)
ttCAGATCAGAGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc > 2:1171406/1‑76 (MQ=255)
tcagatcagaGCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCg > 2:1608293/1‑76 (MQ=255)
cagatcagagCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga < 1:1367034/76‑1 (MQ=255)
cagatcagagCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga > 1:840408/1‑76 (MQ=255)
cagatcagagCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga < 1:622549/76‑1 (MQ=255)
cagatcagagCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga < 1:596308/76‑1 (MQ=255)
gatcagagcGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatg > 2:931198/1‑76 (MQ=255)
atcagagcGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga < 2:529369/76‑1 (MQ=255)
|
AAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGA > REL606/3145912‑3146054
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
