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 |
2,219,353 |
C→T |
33.8% |
L196L (CTC→CTT) |
yhdH → |
predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,219,353 | 0 | C | T | 33.8%
| 44.7
/ 29.5
| 59 | L196L (CTC→CTT) | yhdH | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base C (17/22); new base T (4/16); total (21/38) |
| Fisher's exact test for biased strand distribution p-value = 9.09e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.45e-01 |
GTTTCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCAATTGACACC > minE/2219294‑2219419
|
gTTTCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgat < 1:3248106/69‑1 (MQ=255)
gTTTCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGCTGCTAGCCGTGTTCTCCCTCGtgat < 1:388983/69‑1 (MQ=255)
tttCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:926803/69‑1 (MQ=255)
tttCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:2857552/69‑1 (MQ=255)
tttCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:708983/69‑1 (MQ=255)
tttCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:3158370/69‑1 (MQ=255)
tttCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:1743714/69‑1 (MQ=255)
tCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAg > 1:1567133/1‑69 (MQ=255)
tCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAg < 1:3051063/69‑1 (MQ=255)
tCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAg < 1:386626/69‑1 (MQ=255)
tCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAg > 1:1368292/1‑69 (MQ=255)
tCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAg > 1:2974944/1‑69 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:21888/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:346057/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:2678887/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:331603/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:26091/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:3210666/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:476760/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:553073/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:598740/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:743995/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:1489243/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:778961/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:892415/68‑1 (MQ=255)
gTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:1059874/68‑1 (MQ=255)
tCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:3188830/67‑1 (MQ=255)
tCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGttt < 1:2394115/67‑1 (MQ=255)
gcgAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGTCGTGTTCTCCCTCGTGATGAGTTTGCCg < 1:2469816/69‑1 (MQ=255)
gcgAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCg < 1:3361681/69‑1 (MQ=255)
gcgAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCg < 1:2734160/69‑1 (MQ=255)
gcgAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCg < 1:2038914/69‑1 (MQ=255)
cgAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCg < 1:93875/68‑1 (MQ=255)
gAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:3041168/58‑1 (MQ=255)
gAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGtgatg < 1:2843521/46‑1 (MQ=255)
aaTATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTg > 1:678649/1‑68 (MQ=255)
aaTATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTg > 1:3197370/1‑68 (MQ=255)
aaGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGt > 1:3095259/1‑69 (MQ=255)
aaGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGt > 1:330316/1‑69 (MQ=255)
aaGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGt > 1:838736/1‑69 (MQ=255)
aaGTTTAGGTGCCAGCCGTATTCTTCCTCGCGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGt > 1:892887/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTcc > 1:278065/1‑49 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:1478082/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:2078813/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:2096787/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:2388202/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:923747/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:2653636/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:3401955/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:1333641/1‑69 (MQ=255)
tAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctggg > 1:33074/1‑69 (MQ=255)
gCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTctgggctgg > 1:477093/1‑68 (MQ=255)
cTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTgggg < 1:2396023/69‑1 (MQ=255)
aGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGc < 1:1531192/68‑1 (MQ=255)
aGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGc < 1:897812/68‑1 (MQ=255)
aGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCa < 1:2236750/69‑1 (MQ=255)
aGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCa < 1:474111/69‑1 (MQ=255)
aGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCa < 1:2994910/69‑1 (MQ=255)
ttCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCAATTGaca > 1:1445698/1‑69 (MQ=255)
ctcCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCAATTGACAcc < 1:105281/69‑1 (MQ=255)
|
GTTTCCGGTCGCGAAAGTACCCATGAATATCTGAAAAGTTTAGGTGCTAGCCGTGTTCTCCCTCGTGATGAGTTTGCCGAATCCCGTCCTCTGGAAAAACAAGTCTGGGCTGGGGCAATTGACACC > minE/2219294‑2219419
|
| 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
