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 |
1,177,103 |
G→A |
50.0% |
L192L (TTG→TTA) |
sppA → |
protease IV |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,177,103 | 0 | G | A | 50.0%
| ‑5.2
/ 59.9
| 66 | L192L (TTG→TTA) | sppA | protease IV |
| Reads supporting (aligned to +/- strand): ref base G (25/8); new base A (21/12); total (46/20) |
| Fisher's exact test for biased strand distribution p-value = 4.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01 |
TCTCCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATAAATCTGCCGTTGAAC > minE/1177041‑1177167
|
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1001334/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:2025913/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:657068/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1673277/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:2091245/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:2150541/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:221284/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1508108/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1504267/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:2248519/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1362129/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1210567/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:914705/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:939042/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:556022/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1143718/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1124480/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:385841/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:32703/1‑67 (MQ=255)
tctcCGCAAGGCGTGGTTGATCTGAACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:1083693/1‑67 (MQ=255)
tctcCGCAAGGCGAGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTgg > 1:2306922/1‑67 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:2355768/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:3042798/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:408466/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:2610512/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:2510297/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:2417002/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:612024/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:110738/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:1617574/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:1622288/68‑1 (MQ=255)
tcCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:2010179/68‑1 (MQ=255)
gTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTACTGGATa < 1:171099/58‑1 (MQ=255)
gATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCAcc < 1:824376/69‑1 (MQ=255)
gATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCAcc > 1:1151647/1‑69 (MQ=255)
gATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCAcc > 1:493075/1‑69 (MQ=255)
gATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCAcc > 1:1962396/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGttt > 1:2727500/1‑45 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTTGGTa < 1:1457951/69‑1 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:2526071/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa < 1:329560/69‑1 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:695621/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:432652/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:482965/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:77364/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:74778/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa < 1:677386/69‑1 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:2729615/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:1530605/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:2549588/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa < 1:23960/69‑1 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:3259422/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:1826725/1‑69 (MQ=255)
ccaACGGTCTGTACTACAAATCGTAGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTa > 1:3211418/1‑69 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:2059758/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa < 1:959814/37‑1 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:1172617/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:924861/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:777411/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:1788837/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa < 1:2628379/37‑1 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa < 1:425842/37‑1 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:3430370/1‑37 (MQ=255)
aaCGGTCTGTACTACAAATCGTTGCTGGATAAGCTGa > 1:3299557/1‑37 (MQ=255)
cAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATAAATCTGCCg > 1:1206769/1‑68 (MQ=255)
cGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATAAATCTGCCGTTGAAc > 1:309820/1‑69 (MQ=255)
gCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATaa < 1:1798980/51‑1 (MQ=255)
gCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATaa < 1:2665931/51‑1 (MQ=255)
gCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATaa < 1:1412682/51‑1 (MQ=255)
gCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATaa < 1:866903/51‑1 (MQ=255)
|
TCTCCGCAAGGCGTGGTTGATCTGCACGGCTTTGCCACCAACGGTCTGTACTACAAATCGTTGCTGGATAAGCTGAAAGTTTCCACCCATGTGTTCCGCGTGGGTACGTATAAATCTGCCGTTGAAC > minE/1177041‑1177167
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
