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 |
|
A23 F1 I1 R1
|
14 |
40.5 |
2605368 |
96.4% |
2511574 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,202,382 |
T→G |
T60P (ACC→CCC) |
iclR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,202,382 | 0 | T | G | 97.5%
| 152.1
/ ‑3.7
| 40 | T60P (ACC→CCC) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (21/18); total (21/19) |
| Fisher's exact test for biased strand distribution p-value = 4.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01 |
ATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCA > REL606/4202309‑4202454
|
aTTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGATTAGCAGGCGGTGGGGCg > 1:1224241/1‑76 (MQ=255)
aTTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTCCGGTTAGCAGGCGGGGGGGCg > 1:383224/1‑76 (MQ=255)
ttGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGt < 1:569912/76‑1 (MQ=255)
tGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTg < 1:1057563/76‑1 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCACGCAACCCTGCTGTTGCATTGTGGGTAGCAGGCGGGGGGGCGTGGAAt > 1:484063/1‑76 (MQ=255)
aaTGTCCCAGTTCNCCGACCTGACGCACNAANCCCTGCTGTTGCATTGGGGTTAGCAGGCGGTGGGGCGTGGAAtt < 2:1168647/76‑1 (MQ=255)
aaTGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAtt < 2:299542/76‑1 (MQ=255)
tGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTgg > 2:852630/1‑76 (MQ=255)
tCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGt < 1:1022444/76‑1 (MQ=255)
cccAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTa > 1:597287/1‑76 (MQ=255)
aGTTCGCCGACCTGACGCACGAACCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAAcc < 1:1021946/76‑1 (MQ=255)
tCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCgg > 1:124619/1‑76 (MQ=255)
tCGCCGACCCGACGCACGAAACCCTGCTGTTGCCTTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCgg > 2:1115655/1‑76 (MQ=255)
cGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGc < 2:967749/76‑1 (MQ=255)
cGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGc < 1:1155425/76‑1 (MQ=255)
ccGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCtt < 1:973738/76‑1 (MQ=255)
cTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgc > 1:653248/1‑76 (MQ=255)
tGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcg > 1:297366/1‑76 (MQ=255)
gACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcgc > 2:447235/1‑76 (MQ=255)
cGCACGAAACCTTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCa < 1:197718/76‑1 (MQ=255)
cACGAAACCCTGCTGTTGCATTGTGGTTAGCCGGCGGGGGGGCGTGGAATTGGGAAACCCGGCTTGTTGCACCAGt > 2:850184/1‑76 (MQ=255)
gAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTcc < 2:508653/76‑1 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCg < 2:905381/76‑1 (MQ=255)
aCCCGGTTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGGAACCCGGCTTGTTGCGCCAGTTCCGTg < 1:1277864/76‑1 (MQ=255)
gctgTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGc > 2:1200419/1‑76 (MQ=255)
tgTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCca > 2:454787/1‑76 (MQ=255)
tgTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGCGGGTGCca > 1:191498/1‑76 (MQ=255)
gTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCcac > 2:83781/1‑76 (MQ=255)
ttGCATTGTGGTTAGCAGGCGGTGGGGNGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCcaca > 1:1289582/1‑76 (MQ=255)
tGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCacac < 2:1197566/76‑1 (MQ=255)
gCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACt > 2:267547/1‑76 (MQ=255)
ttGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGACAGTTCCGTGNGTGCCACACtact > 1:163719/1‑73 (MQ=255)
tgtgGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCa > 1:348862/1‑76 (MQ=255)
ggTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTg > 1:467271/1‑76 (MQ=255)
tAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGGCACACTGCCAtt > 1:432653/1‑72 (MQ=255)
tAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAtt < 2:432653/72‑1 (MQ=255)
tAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGAt < 1:126270/76‑1 (MQ=255)
aGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGTGCCAGTTCCGTGAGTGCCACACTGCCATTGGAtt < 1:817939/76‑1 (MQ=255)
gcgggCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTc < 1:1078932/73‑1 (MQ=255)
gCAGGCGGTGGGGCGTGGAATTGGGTAACCCCGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTc < 2:209416/76‑1 (MQ=255)
aGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCgg > 2:1051521/1‑76 (MQ=255)
cGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCaa > 1:618184/1‑76 (MQ=255)
ggTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAAt > 2:534106/1‑76 (MQ=255)
ggggCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCa < 2:422055/76‑1 (MQ=255)
|
ATTGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCCA > REL606/4202309‑4202454
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
