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 |
|
A60 F1 I1 R1
|
14 |
61.1 |
3976207 |
96.5% |
3837039 |
76.0 |
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 | 98.3%
| 239.4
/ ‑4.3
| 58 | T60P (ACC→CCC) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (31/26); total (32/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.59e-01 |
TGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCC > REL606/4202311‑4202453
|
tGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTg > 1:874446/1‑76 (MQ=255)
gCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTgg < 1:1886789/76‑1 (MQ=255)
cccAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGa > 2:883422/1‑76 (MQ=255)
cccAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGa > 2:294532/1‑76 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCAGGAAACCCTGCTGTTGCATTGCGGTTAGCAGGCGGTGGGGCggggggt > 2:1850345/1‑73 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAt < 2:1648290/76‑1 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAt > 2:1982030/1‑76 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAt < 1:140989/76‑1 (MQ=255)
cAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAt > 2:684325/1‑76 (MQ=255)
tGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTgg < 1:1215704/76‑1 (MQ=255)
tGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTgg < 2:354227/76‑1 (MQ=255)
tCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGt > 2:1346154/1‑76 (MQ=255)
cccAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTa > 1:1798899/1‑76 (MQ=255)
ccAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTaa < 2:1951202/76‑1 (MQ=255)
ccAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTaa < 2:462787/76‑1 (MQ=255)
ccAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTaa < 2:63670/76‑1 (MQ=255)
aGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAAcc < 2:261469/76‑1 (MQ=255)
gTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGCGGGGCGGGGGATTGGGGAAccc > 1:936532/1‑76 (MQ=255)
gCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCt < 2:937913/76‑1 (MQ=255)
ccGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCtt < 1:490207/76‑1 (MQ=255)
gccTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCttgtt < 2:1457093/75‑1 (MQ=255)
aCCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCttgtt < 2:1288622/76‑1 (MQ=255)
tGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcg > 1:446271/1‑76 (MQ=255)
tGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcg > 1:730167/1‑76 (MQ=255)
tGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcg < 2:913836/76‑1 (MQ=255)
gACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTgcgc > 1:709708/1‑76 (MQ=255)
cGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCa < 1:1118225/76‑1 (MQ=255)
cGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCa < 1:130062/76‑1 (MQ=255)
cACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGt > 2:844020/1‑76 (MQ=255)
cGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTc > 1:767867/1‑76 (MQ=255)
cGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTc < 2:1770632/76‑1 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCg > 2:209322/1‑76 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCg > 2:1206077/1‑76 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCg > 2:931208/1‑76 (MQ=255)
aaaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACACGGCTTGTTGCGCCAGTTCCg > 2:1184102/1‑76 (MQ=255)
aaaCCCTGCTGTTGCATTGAGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCg > 2:1114411/1‑76 (MQ=255)
aaCCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGt < 1:1818976/76‑1 (MQ=255)
tgTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCGGTTCCGTGAGTGCca > 1:1811769/1‑76 (MQ=255)
tgTTGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCca > 1:1776391/1‑76 (MQ=255)
ttGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCcaca > 1:1130366/1‑76 (MQ=255)
gtGCATTGTGGTTAGCAGGCGGTGGGGCGTGGAAGTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCcaca < 2:204571/75‑1 (MQ=255)
gCATTGTGGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACt < 2:696482/76‑1 (MQ=255)
tgtgGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCa < 2:284596/76‑1 (MQ=255)
gtgGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAt > 1:124192/1‑76 (MQ=255)
tgGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAtt < 2:1239560/76‑1 (MQ=255)
tgGTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCAtt > 1:1679845/1‑76 (MQ=255)
gTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTgg > 1:1387386/1‑76 (MQ=255)
gTTAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTgg < 2:75662/76‑1 (MQ=255)
ttAGCAGGCGGTGGGGCGTGGAATTGGGTAGCCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGa < 1:1786632/76‑1 (MQ=255)
ttAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGa > 1:577182/1‑76 (MQ=255)
tgaGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGa < 1:1849894/74‑1 (MQ=255)
tAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGAt > 2:1967076/1‑76 (MQ=255)
tAGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGAt > 1:120333/1‑76 (MQ=255)
aGCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGAtt > 1:710137/1‑76 (MQ=255)
gCAGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTc < 2:1920705/76‑1 (MQ=255)
cggCCGTGGGGCCTTGAATTAGGGTACCCGGCTTGTTGGGGCAGTTCCGGGGAGGGCGCACTGCCATTGGATTCgg < 2:450158/75‑1 (MQ=255)
aGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCgg > 1:228143/1‑76 (MQ=255)
aGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCgg > 2:620940/1‑76 (MQ=255)
aGGCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCgg > 2:1176146/1‑76 (MQ=255)
ggCGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGc < 2:726216/76‑1 (MQ=255)
cGGTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCaa > 1:1798183/1‑76 (MQ=255)
ggTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAAt > 2:902335/1‑76 (MQ=255)
gTGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATc > 2:293215/1‑76 (MQ=255)
tGGGGCGTGGAATTGGGTACCCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATcc < 1:685571/76‑1 (MQ=255)
tGGGGCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATcc > 2:49230/1‑76 (MQ=255)
|
TGCCCAATGTCCCAGTTCGCCGACCTGACGCACGAAACCCTGCTGTTGCATTGTGGTTAGCAGGCGGTGGGTCGTGGAATTGGGTAACCCGGCTTGTTGCGCCAGTTCCGTGAGTGCCACACTGCCATTGGATTCGGCAATCC > REL606/4202311‑4202453
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
