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 |
|
A66 F1 I1 R1
|
19 |
57.4 |
3651244 |
97.1% |
3545357 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,932 |
C→T |
T23T (ACC→ACT) |
rpoD → |
RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,932 | 0 | C | T | 97.3%
| 281.2
/ ‑0.5
| 73 | T23T (ACC→ACT) | rpoD | RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base C (0/2); new base T (36/35); total (36/37) |
| Fisher's exact test for biased strand distribution p-value = 4.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.21e-01 |
TCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATG > REL606/3145860‑3146004
|
tCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTAt < 2:1110560/76‑1 (MQ=255)
tCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTAt < 1:739947/76‑1 (MQ=255)
cTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATg > 1:1277148/1‑76 (MQ=255)
ggAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAg > 2:571385/1‑76 (MQ=255)
ggAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAg < 1:405677/76‑1 (MQ=255)
gAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAgg < 2:1505796/76‑1 (MQ=255)
cAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCa < 1:573079/76‑1 (MQ=255)
aaaaCCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCaa > 2:104271/1‑76 (MQ=255)
aCCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGa < 2:1174033/76‑1 (MQ=255)
cccGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGAc > 1:1821564/1‑76 (MQ=255)
ccGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGAcc > 1:674083/1‑76 (MQ=255)
cGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCa < 2:940704/76‑1 (MQ=255)
cAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATc > 2:59577/1‑76 (MQ=255)
cAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATc > 2:1441903/1‑76 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 2:49559/76‑1 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 2:363302/76‑1 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 2:25338/76‑1 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg > 1:1547704/1‑76 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 1:545753/76‑1 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 2:1375540/76‑1 (MQ=255)
gTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTg < 1:723695/76‑1 (MQ=255)
cacaGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGcc > 1:717373/1‑76 (MQ=255)
cTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAg > 2:1774941/1‑76 (MQ=255)
tGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGa > 1:1739920/1‑76 (MQ=255)
tGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGa > 2:1045662/1‑76 (MQ=255)
gAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATCCCTAGCTCAATGACCATCTGCCGGAAGat > 1:1606635/1‑76 (MQ=255)
aaaCTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGata > 2:643080/1‑76 (MQ=255)
aaaCTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGata < 1:1031934/76‑1 (MQ=255)
cttcttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcg < 1:330972/76‑1 (MQ=255)
cttcttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcg > 1:1777776/1‑76 (MQ=255)
cttcttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcg > 2:1663935/1‑76 (MQ=255)
cttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcgtcg > 2:894337/1‑76 (MQ=255)
cttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcgtcg < 1:1454766/76‑1 (MQ=255)
cttGTCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATAtcgtcg > 2:868805/1‑76 (MQ=255)
tCACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtc > 1:339858/1‑76 (MQ=255)
cACCCGTGGTAAGGAGCAAGGCTATCTGGCTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtca < 2:808277/76‑1 (MQ=255)
cACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtca < 1:702483/76‑1 (MQ=255)
cACCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtca < 1:948424/76‑1 (MQ=255)
aCCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcag < 1:825276/76‑1 (MQ=255)
aCCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcag < 1:825297/76‑1 (MQ=255)
aCCCGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcag < 1:114444/76‑1 (MQ=255)
ccGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcagat < 2:1234059/76‑1 (MQ=255)
ccGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcagat < 2:1234070/76‑1 (MQ=255)
cGTGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcagatc < 2:1679623/76‑1 (MQ=255)
tGGTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcagatcag > 1:1277483/1‑76 (MQ=255)
ggTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATtcagatcaga > 1:1471538/1‑76 (MQ=255)
gTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTcagatcagat < 2:1230601/76‑1 (MQ=255)
gTAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTcagatcagat > 2:1525011/1‑76 (MQ=255)
tAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCagatcagatc < 1:1454492/76‑1 (MQ=255)
tAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCagatcagatc < 1:244249/76‑1 (MQ=255)
tAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCagatcagatc < 2:128818/76‑1 (MQ=255)
tAAGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCagatcagatc < 2:905223/76‑1 (MQ=255)
aaGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGCTTCAGATCAGATCg > 2:842506/1‑76 (MQ=255)
aaGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCg > 2:842485/1‑76 (MQ=255)
aaGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCg < 1:522958/76‑1 (MQ=255)
aGGAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGa > 2:498730/1‑76 (MQ=255)
gAGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAg > 2:437656/1‑76 (MQ=255)
aGCAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGa < 1:168720/76‑1 (MQ=255)
cAAGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGAca > 2:483531/1‑76 (MQ=255)
cAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGAca < 2:1584708/76‑1 (MQ=255)
aaGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGAcat > 2:592959/1‑76 (MQ=255)
aaGGCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGAcat < 1:1186192/76‑1 (MQ=255)
gCTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGAcatcat < 1:1110436/76‑1 (MQ=255)
cTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACatcatc > 2:1470304/1‑76 (MQ=255)
cTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACatcatc > 2:1116806/1‑76 (MQ=255)
cTATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACatcatc > 1:779261/1‑76 (MQ=255)
tATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATcc > 2:414022/1‑76 (MQ=255)
tATCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATcc > 1:1432556/1‑76 (MQ=255)
aTCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGACATCGTCGATTCAGATCAGATCGAAGACATCATCCa > 1:979692/1‑76 (MQ=255)
tCTGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCaa > 1:886695/1‑76 (MQ=255)
tGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAAt > 2:1271291/1‑76 (MQ=255)
tGACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAAt < 1:882581/76‑1 (MQ=255)
gACTTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATg < 1:206836/76‑1 (MQ=255)
|
TCTTATGGAGCAAAACCCGCAGTCACAGCTGAAACTTCTTGTCACCCGTGGTAAGGAGCAAGGCTATCTGACCTATGCCGAGGTCAATGACCATCTGCCGGAAGATATCGTCGATTCAGATCAGATCGAAGACATCATCCAAATG > REL606/3145860‑3146004
|
| 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
