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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
335,821 |
T→G |
59.7% |
R243R (CGA→CGC) |
ybaP ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 335,821 | 0 | T | G | 59.7%
| 40.9
/ 54.8
| 67 | R243R (CGA→CGC) | ybaP | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (3/24); new base G (16/24); total (19/48) |
| Fisher's exact test for biased strand distribution p-value = 1.28e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.73e-01 |
CATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCAGCACATCG > minE/335764‑335887
|
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:627583/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:425785/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:196225/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:1990377/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:2283003/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:2351681/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:3143533/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:124187/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:273163/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:3087518/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:2855480/69‑1 (MQ=255)
cATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:3083545/69‑1 (MQ=255)
tGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCCGGCGGCATg < 1:336186/69‑1 (MQ=255)
tGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCCGGCGGCATg < 1:2858878/69‑1 (MQ=255)
aGGTGTAGTGCACCGACCGCGACCACATATCGCCCcggcgg < 1:451596/41‑1 (MQ=255)
cACCGAGCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCt > 1:440796/1‑69 (MQ=255)
cACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGcc > 1:1754542/1‑54 (MQ=255)
cACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCt > 1:1630654/1‑69 (MQ=255)
cACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCt < 1:3410405/69‑1 (MQ=255)
cACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCt < 1:1537217/69‑1 (MQ=255)
cACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCt < 1:1522695/69‑1 (MQ=255)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:3186393/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:2918948/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:1267840/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:1075279/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:2545886/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:49848/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:1606998/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:1498672/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:1999745/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:3405184/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:411711/43‑1 (MQ=38)
ccgactgCGACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:418484/43‑1 (MQ=38)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:1471915/69‑1 (MQ=255)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:3158607/69‑1 (MQ=255)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:1230627/69‑1 (MQ=255)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:928939/69‑1 (MQ=255)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:1538050/69‑1 (MQ=255)
accgCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc < 1:929414/69‑1 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:2568811/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:823533/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:846401/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1774170/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1090771/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:110815/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:13407/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1511213/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1528630/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1650165/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:1769842/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:2974093/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:2932660/2‑67 (MQ=255)
tgcgACCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:2607545/2‑67 (MQ=255)
tgcgACCACATAGCGCCACGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGc > 1:619087/2‑67 (MQ=255)
tgcgACCACATAGCG‑CCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATc > 1:1630769/2‑69 (MQ=255)
gACCACATAGCGCCCCGGCGGCATGGCGCGTAAtt < 1:2103158/35‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:3269013/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:1159494/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:837367/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:2777449/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:1386514/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:3108189/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:3153274/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:2375275/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:2251362/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:1945042/67‑1 (MQ=255)
aCCACATAGCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCa < 1:3186593/67‑1 (MQ=255)
tCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCAGCACATCg > 1:1163228/1‑67 (MQ=255)
tCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCAGCACATCg > 1:3022888/1‑67 (MQ=255)
|
CATTTGCGGCAAATTCCCTTCTCCATACAGGTGTAGTGCACCGACCGCGACCACATATCGCCCCGGCGGCATGGCGCGTAATTTATCCCGCCAGGCGAGATTTCGCTGATGCATCAGCACATCG > minE/335764‑335887
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
