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 |
|
A18 F1 I1 R1
|
18 |
50.6 |
3235256 |
96.4% |
3118786 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,998 |
C→T |
I45I (ATC→ATT) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,998 | 0 | C | T | 98.4%
| 244.3
/ ‑3.6
| 64 | I45I (ATC→ATT) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (33/30); total (33/31) |
| Fisher's exact test for biased strand distribution p-value = 4.84e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.94e-01 |
TCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGA > REL606/3145926‑3146069
|
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCNGATCGAAGACATCATTCaa < 1:1506966/76‑1 (MQ=255)
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCaa < 1:64274/76‑1 (MQ=255)
tCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCaa > 1:1359264/1‑76 (MQ=255)
cTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGTCATCATTCaaa > 1:217671/1‑76 (MQ=255)
tGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAAt > 1:1171241/1‑76 (MQ=255)
gACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATg > 1:662604/1‑76 (MQ=255)
tcTATGCCGAGGTCAATGACCATCTGCGGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGAt < 1:274064/75‑1 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGAt > 2:1438310/1‑76 (MQ=255)
ccTATGCCGAGGTCAATGACCATCTGCCGGAAGATAGCGTCGATTCAGATCAGATCGNAGACATCATTCAAATGAt < 1:1545282/76‑1 (MQ=255)
cTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATc < 2:637675/76‑1 (MQ=255)
tATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCa < 2:126815/76‑1 (MQ=255)
tATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCa < 2:1404266/76‑1 (MQ=255)
aTGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCaa < 1:556742/76‑1 (MQ=255)
aTGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCaa < 2:1011505/76‑1 (MQ=255)
gCCGAGGTCAATGNCCATCTGCCGGAAGATATCGTCGATTCAGATTAGATCGAAGACATCATTCAAATGATCAACg < 2:1483085/76‑1 (MQ=255)
gCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACg < 2:77984/76‑1 (MQ=255)
ccGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGa < 2:1219348/76‑1 (MQ=255)
gAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACa > 2:1142707/1‑76 (MQ=255)
gTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATgg < 1:1176338/76‑1 (MQ=255)
cAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGc > 2:868391/1‑76 (MQ=255)
cAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGc > 2:531216/1‑76 (MQ=255)
cAATGACCATCTGCCGGAAGAAATGGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGc < 1:1518437/76‑1 (MQ=255)
aaTGACCATCTGCCGGAAGATATCGTCGATTCANTTAAGATCGAAGACATCATTCAAATGATCAACGACATGGGCa > 2:1377354/1‑76 (MQ=255)
tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCAtt < 2:298789/76‑1 (MQ=255)
tGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCAtc < 2:1490871/76‑2 (MQ=255)
aCCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCa < 1:1260231/76‑1 (MQ=255)
ccATCTGCNGGAAGATATCGTCGATTCAGATCAGATCGATGACATCATTCAAATGATCAACGACATGGGCATTCAg < 1:1428528/76‑1 (MQ=255)
ccATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAg < 1:428464/76‑1 (MQ=255)
aTCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGt > 1:842337/1‑76 (MQ=255)
cTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGa > 2:1121345/1‑76 (MQ=255)
cTGCCGGAAAATATCGTCGATTCNGATCANATCGAGGACATCATNCAGATGCTCAACGACACGGGCATTCAGGTGa > 2:201054/1‑76 (MQ=255)
gCCGGAAGATATTGTCGATTCAGATCAGATCGNAGCCATCANTCAAAGGATCAACGACATGNGCATTCAGGTGATg > 2:1331545/1‑76 (MQ=255)
gCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATg > 2:78570/1‑76 (MQ=255)
ccGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATgg > 2:704570/1‑76 (MQ=255)
cGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGga < 1:868391/76‑1 (MQ=255)
ggAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGgaa > 2:765921/1‑76 (MQ=255)
ggAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGgaa < 1:1240031/76‑1 (MQ=255)
gAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGgaag > 1:277571/1‑76 (MQ=255)
gAAGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATGCAGGTGATGgaag < 1:114533/76‑1 (MQ=255)
aaGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGgaaga < 2:1138046/76‑1 (MQ=255)
aGATATCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGgaagaa > 1:613707/1‑76 (MQ=255)
atCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc > 1:1219451/1‑76 (MQ=255)
atCGTCGATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCAc > 1:1180016/1‑76 (MQ=255)
cgtcaATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCg > 2:1594402/1‑76 (MQ=255)
cgATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGAt < 1:1194641/76‑1 (MQ=255)
cgATTCAGACCAGATCGAAGACANCATTCNAATGACCAACGACANGGGCATACAGGTGATGAAAGAAGCACCGGAt > 2:210169/1‑76 (MQ=255)
gATTCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATg < 2:1609536/76‑1 (MQ=255)
ttCAGATCAGATCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGcc > 2:1494434/1‑76 (MQ=255)
ttCAGATCAGATCGAAGACATCATTCAAATGANCATCGACANGGGCAATCAGGTGATGGAANAAGCACCGGATGcc > 2:1331888/1‑76 (MQ=255)
tcagatcagaTCGNAGACATCATTCAAANGANCAACGACATGGGCATTGAGGTGATGGAAGAAGCACCGGATGCCg < 2:1461827/76‑1 (MQ=255)
tcagatcagaTCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCg > 1:478177/1‑76 (MQ=255)
cagatcagatCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga < 2:169255/76‑1 (MQ=255)
cagatcagatCGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCga > 2:32103/1‑76 (MQ=255)
atcagatcGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCgatga > 1:984949/1‑76 (MQ=255)
tcagaacGAAGACATCATTCAAATGCTCAACAATATGGGCATTCAGGTGATGGAAGAAGCGCCGGATGCCgatgat < 2:1584388/76‑1 (MQ=255)
atcGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGa > 2:461693/1‑76 (MQ=255)
tcGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGAt > 2:41269/1‑76 (MQ=255)
tcGAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGAt < 2:740092/76‑1 (MQ=255)
gAAGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgc > 1:1268262/1‑76 (MQ=255)
aaGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgct < 2:476162/76‑1 (MQ=255)
aaGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgct > 2:111905/1‑76 (MQ=255)
aaGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgat > 1:879510/1‑74 (MQ=255)
aaGACATCATTCAAATGATCAAAGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgct > 2:463109/1‑76 (MQ=255)
ataCATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgctg > 1:452087/3‑76 (MQ=255)
aGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgctg < 2:682639/76‑1 (MQ=255)
aGACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgctg > 1:1196888/1‑76 (MQ=255)
gACATCATTCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATgctgg < 2:403063/76‑1 (MQ=255)
tcattCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGa < 2:608409/76‑1 (MQ=255)
|
TCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATGATCAACGACATGGGCATTCAGGTGATGGAAGAAGCACCGGATGCCGATGATCTGATGCTGGCTGA > REL606/3145926‑3146069
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
