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 |
|
A22 F1 I1 R1
|
17 |
44.7 |
2806446 |
96.5% |
2708220 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,570,909 |
T→A |
I37N (ATC→AAC) |
uspA → |
universal stress global response regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,570,909 | 0 | T | A | 97.8%
| 168.5
/ ‑3.6
| 46 | I37N (ATC→AAC) | uspA | universal stress global response regulator |
| Reads supporting (aligned to +/- strand): ref base T (0/1); major base A (16/28); minor base G (0/1); total (16/30) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.04e-01 |
CCCGGAAAGCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGATCCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGAAAC > REL606/3570838‑3570980
|
cccGGAAAGCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCAc < 1:524291/76‑1 (MQ=255)
cGGAAAGCAAAGTTCTGGTAGAGAAAGCAATCTCTATGGCTCGCCCCCACAATGCGAAAGTTTCTCTGAACCACGt > 1:495288/1‑76 (MQ=255)
gAAAGCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAg < 1:546908/76‑1 (MQ=255)
aaaGCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCCACAATGCGAAAGTTTCTCTGAACCACGTAGa > 2:344050/1‑76 (MQ=255)
gCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGt < 1:986066/76‑1 (MQ=255)
cAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAAAGCGAAAGTTTCTCTGAACCACGTAGATGTa > 1:914950/1‑76 (MQ=255)
aaaGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTaa < 1:767119/76‑1 (MQ=255)
aaaGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTaa < 1:242529/76‑1 (MQ=255)
gTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCCACAATGCGAAAGTTTCTCTGAAACACGTAGATGTaaaat > 1:272650/1‑74 (MQ=255)
tCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAactac < 1:340230/76‑1 (MQ=255)
cTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCCACCATGCGAAAATTTCTCTGAACCACGTAGATGNAAactact > 1:1235777/1‑76 (MQ=255)
ggTAGAGANAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTActct < 1:1234809/76‑1 (MQ=255)
gTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTg < 2:504427/76‑1 (MQ=255)
gTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTg < 1:591979/76‑1 (MQ=255)
agagAAAGCAGTCTCTATGGCTCGCCCCTACCATGCGAAAATTTTTCTGATCCACGGAGATGTAAACTACTCTGAc > 1:1067404/1‑76 (MQ=255)
gagaAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGAcc < 1:326524/76‑1 (MQ=255)
gagaAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGAcc < 1:668094/76‑1 (MQ=255)
agaAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCt < 1:847387/76‑1 (MQ=255)
gaAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCta < 2:1052301/76‑1 (MQ=255)
gaAAGCAGTATCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACCCTGACCta < 1:47995/76‑1 (MQ=255)
aaaGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCtat < 1:749984/76‑1 (MQ=255)
ctctATGGCTCGCCCCCACAATGCGAAAGTTTCTCTTAACCACGTAGATGTAAACTACTCTGACCTATACACCggg > 2:1010788/1‑76 (MQ=255)
tctATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAGCCACGTAGATGTAAACTACTCTGACCTATACACCGGGc < 2:638153/76‑1 (MQ=255)
tctATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGc > 2:13267/1‑76 (MQ=255)
ctATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCt > 2:538043/1‑76 (MQ=255)
ctATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCt > 2:1010390/1‑76 (MQ=255)
aTGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTa < 2:569310/76‑1 (MQ=255)
aTGGATCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAAGTACTCTGACCTATACACCTGGCNTa > 2:1318390/1‑76 (MQ=255)
tGGCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTAt < 2:412208/76‑1 (MQ=255)
gCTCGCCCCTACAATGCGAAAGTTTCTCTGATCCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTg < 2:221674/76‑1 (MQ=255)
gCTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATAAACCGGGCTTATTg > 1:994175/1‑76 (MQ=255)
cTCGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGa > 2:1146007/1‑76 (MQ=255)
cGCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGAtg > 2:1133121/1‑76 (MQ=255)
gCCCCTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGAtgt < 2:550836/76‑1 (MQ=255)
ccccTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGAtgtg < 2:571603/76‑1 (MQ=255)
cccTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGa < 2:375354/76‑1 (MQ=255)
ccTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGaa > 1:854267/1‑76 (MQ=255)
cTACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAAt > 1:796408/1‑76 (MQ=255)
tACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATc < 2:568621/76‑1 (MQ=255)
tACAATGCGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATc < 1:1088497/76‑1 (MQ=255)
cAANGCACAAGTTTCTCTGAACCAGGTAGATGTAAACTACTCTGACCTATACATCGGGCTTATTGATGTGAATTTg < 2:1270147/76‑1 (MQ=255)
cGAAAGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGa > 2:980723/1‑76 (MQ=255)
aGTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATg > 2:435113/1‑76 (MQ=255)
gTTTCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGc < 1:1157069/76‑1 (MQ=255)
tttCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCa > 2:687562/1‑76 (MQ=255)
ttCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAg > 1:987156/1‑76 (MQ=255)
ttCTCTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAg < 1:778126/76‑1 (MQ=255)
tctcTGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGa > 1:236069/1‑76 (MQ=255)
tctGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGaaa < 1:198317/76‑1 (MQ=255)
tctGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGaaa < 1:104899/76‑1 (MQ=255)
ctGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGAAAc < 1:871354/76‑1 (MQ=255)
ctGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGAAAc > 1:781617/1‑76 (MQ=255)
ctGAACCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGAAAc > 1:549229/1‑76 (MQ=255)
|
CCCGGAAAGCAAAGTTCTGGTAGAGAAAGCAGTCTCTATGGCTCGCCCCTACAATGCGAAAGTTTCTCTGATCCACGTAGATGTAAACTACTCTGACCTATACACCGGGCTTATTGATGTGAATCTGGGTGATATGCAGAAAC > REL606/3570838‑3570980
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
