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 |
|
A142 F1 I1 R1
|
21 |
42.6 |
2691336 |
96.3% |
2591756 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,145,823 |
G→A |
intergenic (+154/‑41) |
dnaG → / → rpoD |
DNA primase/RNA polymerase sigma factor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,145,823 | 0 | G | A | 97.4%
| 132.2
/ ‑3.4
| 39 | intergenic (+154/‑41) | dnaG/rpoD | DNA primase/RNA polymerase sigma factor |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (12/26); total (12/27) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01 |
CCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAA > REL606/3145750‑3145893
|
cccTCGTAATTATCGTTNGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGATCAATCAcc > 1:174109/1‑76 (MQ=255)
cccTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCAcc < 1:998818/76‑1 (MQ=255)
cTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCa < 1:1013583/76‑1 (MQ=255)
cGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTTAGAGTTAACGGNTGAAGGACATCGGGTCAATCACCCAac < 1:1169516/76‑1 (MQ=255)
cGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAac > 2:1113385/1‑76 (MQ=255)
gTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGTGTTAACGGCTGAAGGACATCGGGTCAATCACCCAaca < 2:386500/76‑1 (MQ=255)
gTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGTGTCAATCACCCAaca < 1:122743/76‑1 (MQ=255)
gTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAaca > 1:862594/1‑76 (MQ=255)
tAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAacac > 2:1270194/1‑76 (MQ=255)
tAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAacac > 2:1201042/1‑76 (MQ=255)
aaTTATCGTTGGCGGGAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACAcc < 1:1102514/76‑1 (MQ=255)
ttATCGTTGGCGGTATACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCaa < 1:1105759/76‑1 (MQ=255)
ttATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCaa > 2:165133/1‑76 (MQ=255)
ttATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCaa < 1:867968/76‑1 (MQ=255)
tccGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAAcc < 2:602431/74‑1 (MQ=255)
tCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCt < 1:726004/76‑1 (MQ=255)
tGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATg < 2:362729/76‑1 (MQ=255)
ggTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAAt < 2:1148002/76‑1 (MQ=255)
gTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATa > 1:640502/1‑76 (MQ=255)
tAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATaa > 1:646446/1‑76 (MQ=255)
aaaCAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAg < 1:527079/76‑1 (MQ=255)
acCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTgg < 2:1177427/76‑1 (MQ=255)
gTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATa < 2:268192/76‑1 (MQ=255)
ggATTTCAGCGTTAACGTCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCGTGAAATAAGTGTGGATACCg > 1:1331849/1‑76 (MQ=255)
aTTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTc > 1:640537/1‑76 (MQ=255)
tCAGCGTTAACGTCTCAAGGACATCGGGTGAATCACCCATAACCAACCTCATGAAATCAGTGTGGATGCCGTCTTa < 2:30369/76‑1 (MQ=255)
gTTAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAg < 2:186063/76‑1 (MQ=255)
ttAACGGCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGc < 2:383195/76‑1 (MQ=255)
ggCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAc < 1:1026172/76‑1 (MQ=255)
gCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAcc < 2:960236/76‑1 (MQ=255)
gCTGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAAcc > 1:463626/1‑76 (MQ=255)
tGAAGGACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCg < 1:1015223/76‑1 (MQ=255)
ggACATCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGt < 1:788618/76‑1 (MQ=255)
aCATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTca < 2:236308/76‑1 (MQ=255)
aTCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTcaca < 1:555469/76‑1 (MQ=255)
aTCGGGTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGGcaca < 2:918606/76‑1 (MQ=255)
ggTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTg < 1:314552/76‑1 (MQ=255)
ggTCAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTg < 1:238726/76‑1 (MQ=255)
cAATCACCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGaaa > 2:1275801/1‑76 (MQ=255)
|
CCCTCGTAATTATCGTTGGCGGTAAACAACCGTTGGATTTCAGCGTTAACGGCTGAAGGACATCGGGTCAATCGCCCAACACCAACCTCATGAAATAAGTGTGGATACCGTCTTATGGAGCAAAACCCGCAGTCACAGCTGAAA > REL606/3145750‑3145893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
