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 |
1,845,292 |
G→A |
51.8% |
P235S (CCG→TCG) |
cysD ← |
sulfate adenylyltransferase, subunit 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,845,292 | 0 | G | A | 51.8%
| ‑4.7
/ 49.2
| 57 | P235S (CCG→TCG) | cysD | sulfate adenylyltransferase, subunit 2 |
| Reads supporting (aligned to +/- strand): ref base G (11/16); new base A (22/7); total (34/23) |
| Fisher's exact test for biased strand distribution p-value = 1.37e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01 |
CAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGAACCGGACGTTC > minE/1845233‑1845358
|
cAGCGGCCAGCTGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:2099748/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc > 1:1125582/1‑69 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc > 1:466569/1‑69 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:388127/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:3113942/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:2896096/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:2703886/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:2103721/69‑1 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc > 1:1619137/1‑69 (MQ=255)
cAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:1392534/69‑1 (MQ=255)
gcagcCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTc < 1:1317770/60‑1 (MQ=255)
gTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCatcaatc > 1:122899/1‑69 (MQ=255)
gTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCatcaatc > 1:377943/1‑69 (MQ=255)
gTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCatcaat > 1:521187/1‑68 (MQ=255)
gAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAatcatcat < 1:223156/69‑1 (MQ=255)
gAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAatcatcat < 1:975768/69‑1 (MQ=255)
aCGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCaa < 1:2691315/69‑1 (MQ=255)
cATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAatcatcat < 1:1132807/60‑1 (MQ=255)
cGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTcg > 1:3313215/1‑69 (MQ=255)
cGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTcg > 1:897425/1‑69 (MQ=255)
cGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTcg > 1:2858576/1‑69 (MQ=255)
cGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTcg > 1:1602721/1‑69 (MQ=255)
cGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTcg > 1:2704760/1‑69 (MQ=255)
ttttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:2088270/69‑1 (MQ=255)
ttttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:2895425/69‑1 (MQ=255)
ttttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:2886547/69‑1 (MQ=255)
ttttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:19629/69‑1 (MQ=255)
ttttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:749442/69‑1 (MQ=255)
tttttAATCACTTCGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:3100896/68‑1 (MQ=255)
tCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGa < 1:388012/68‑1 (MQ=255)
tCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGa < 1:3202641/68‑1 (MQ=255)
tCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGa < 1:858823/68‑1 (MQ=255)
cACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGa < 1:1289153/67‑1 (MQ=255)
cGCCCGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTcgcg < 1:2146372/55‑1 (MQ=255)
cccGCTTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:1335153/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCg > 1:854625/1‑64 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGAc > 1:1788984/1‑67 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:833126/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:553793/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:601418/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:635553/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:990884/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:846047/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:987563/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:1339143/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:101849/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:120868/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:2858479/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:1264233/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:2615273/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:2411541/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:2310490/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:220660/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:220109/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:1965156/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTCCAGAACCGGACg > 1:1521937/1‑68 (MQ=255)
cccGATTGCAGGTTGATACGGTTGTCATCAATCATCATCAGCATACCGTCGCGTTACAGAACCGGACg > 1:1519777/1‑68 (MQ=255)
ggTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGAACCGGACGTTc > 1:793767/1‑68 (MQ=255)
|
CAGCGGCCAGCAGCCCAGCGTACGGAAACGCACCATCCGTTTTTTAATCACTTCGCCCGGTTGCAGGTCGATACGGTTGTCATCAATCATCATCAACATACCGTCGCGTTCCAGAACCGGACGTTC > minE/1845233‑1845358
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
