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 |
|
A87 F1 I1 R1
|
13 |
46.2 |
2986023 |
95.8% |
2860610 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,202,404 |
T→G |
Q52H (CAA→CAC) |
iclR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,202,404 | 0 | T | G | 97.5%
| 162.1
/ ‑4.1
| 40 | Q52H (CAA→CAC) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (24/15); total (25/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.40e-01 |
GACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCACGC > REL606/4202332‑4202476
|
gACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCgtgt > 2:851067/1‑76 (MQ=255)
cTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGAGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTgc > 2:766365/1‑76 (MQ=255)
tGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTgcg > 1:1018363/1‑76 (MQ=255)
gACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTgcgc > 1:1151007/1‑76 (MQ=255)
cGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCa < 2:708233/76‑1 (MQ=255)
cGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCa > 2:294307/1‑76 (MQ=255)
gCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCaa < 2:633160/76‑2 (MQ=255)
gCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGGGGGACGTGGAATTGGGTAACCCGGCGTGTTGCGcccg > 2:935142/1‑74 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCg > 1:1019150/1‑76 (MQ=255)
aaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGt < 2:1000910/76‑1 (MQ=255)
ctgTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGcc > 2:1445482/1‑76 (MQ=255)
ctgTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGcc > 2:486194/1‑76 (MQ=255)
ctgTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGAGTGGTGCGCCAGTCCCGTGAGTGcc > 2:796339/1‑76 (MQ=255)
tgTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCca < 2:578653/76‑1 (MQ=255)
gTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCcac > 1:566000/1‑76 (MQ=255)
tGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCacac > 1:706937/1‑76 (MQ=255)
gCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACt < 1:819223/76‑1 (MQ=255)
cATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTg < 2:153276/76‑1 (MQ=255)
aTTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGCGAGTGCCACACTGc > 2:373167/1‑76 (MQ=255)
tgtgGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGTGTGCCACACTGCCa < 1:793527/76‑1 (MQ=255)
gtgGTTAGCAGGCGGTGGGTCGTGGAAGTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAt < 1:1337787/76‑1 (MQ=255)
tgGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAtt > 1:149715/1‑76 (MQ=255)
aGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCgg > 1:587388/1‑76 (MQ=255)
aGGCGGTGGGTCGTGGAATTGGGTAACCCGGCGTGTTCCGCAAGTTCCGCGAGTCCCAAACTGCCATCGGATCCga > 1:1428849/1‑75 (MQ=255)
gTGGGTCGTGGAATTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATc > 1:407739/1‑76 (MQ=255)
naaTTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTa > 1:1135028/2‑76 (MQ=255)
aaTTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTaa > 2:1141156/1‑76 (MQ=255)
aTTGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAAt < 1:29896/76‑1 (MQ=255)
tGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAAttt < 1:739574/76‑1 (MQ=255)
tGGGTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAAttt < 2:917688/76‑1 (MQ=255)
ggTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCa > 2:1991/1‑76 (MQ=255)
ggTAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCa > 1:413169/1‑76 (MQ=255)
tAACCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAgg < 1:720276/76‑1 (MQ=255)
aaCCCGGCGTGTTNCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGc > 1:1004972/1‑76 (MQ=255)
aaCCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGc > 1:870868/1‑76 (MQ=255)
aaCCCGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTGCAGGc > 2:1477921/1‑76 (MQ=255)
cccGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCa < 1:554190/76‑1 (MQ=255)
cGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCTCTCCAGTAATTTCAGGCCAcg < 2:413919/76‑1 (MQ=255)
cGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCAcg > 2:1106222/1‑76 (MQ=255)
cGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCAcg < 1:581788/76‑1 (MQ=255)
cGGCGTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCAcg > 1:517230/1‑76 (MQ=255)
ggCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCAcgc > 1:278083/1‑76 (MQ=255)
|
GACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCACTCCAGTAATTTCAGGCCACGC > REL606/4202332‑4202476
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
