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 |
|
A25 F36 I0 R2
|
1302 |
104.9 |
4551290 |
96.3% |
4382892 |
111.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,247,626 |
G→A |
8.3% |
intergenic (‑250/+70) |
treA ← / ← dhaM |
periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,247,626 | 0 | G | A | 8.3%
| 148.5
/ 4.2
| 48 | intergenic (‑250/+70) | treA/dhaM | periplasmic trehalase/putative dihydroxyacetone‑specific PTS enzymes: HPr, EI components |
| Reads supporting (aligned to +/- strand): ref base G (22/22); new base A (2/2); total (24/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
GAAAAGGGAATTAAAGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTAT > NC_000913/1247495‑1247758
|
gAAAAGGGAATTAAAGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCAtt < 4:1105526/148‑1 (MQ=255)
aGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAg < 2:634085/136‑1 (MQ=255)
aGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAg > 1:634085/1‑136 (MQ=255)
taaataaCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAg < 3:1112061/113‑1 (MQ=255)
taaataaCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAg > 4:1112061/1‑113 (MQ=255)
aataaCGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGa > 3:761133/1‑148 (MQ=255)
aaaTAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAgg > 4:266182/1‑102 (MQ=255)
aaaTAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAgg < 3:266182/102‑1 (MQ=255)
tCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGc < 1:504869/123‑1 (MQ=255)
tCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGc > 2:504869/1‑123 (MQ=255)
aaTAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc > 4:1102673/1‑128 (MQ=255)
aaTAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGAc < 3:1102673/128‑1 (MQ=255)
cGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGt < 4:761133/148‑1 (MQ=255)
tGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACa > 2:808842/1‑120 (MQ=255)
tGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACa < 1:808842/120‑1 (MQ=255)
tttATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGa < 3:198519/127‑1 (MQ=255)
tttATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGa > 4:198519/1‑127 (MQ=255)
tttATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATc > 4:533288/1‑134 (MQ=255)
tttATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATc < 3:533288/134‑1 (MQ=255)
taGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAAGTAGTTAAAAACCATTAg > 4:446596/1‑89 (MQ=255)
taGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAAGTAGTTAAAAACCATTAg < 3:13303/89‑1 (MQ=255)
taGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAAGTAGTTAAAAACCATTAg < 3:446596/89‑1 (MQ=255)
taGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAAGTAGTTAAAAACCATTAg > 4:13303/1‑89 (MQ=255)
ccagccagCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTa > 2:20583/1‑85 (MQ=255)
ccagccagCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTa < 1:20583/85‑1 (MQ=255)
gccagcGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGAt < 3:318568/117‑1 (MQ=255)
gccagcGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGAt > 4:318568/1‑117 (MQ=255)
cggcgTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAAt < 2:735268/90‑1 (MQ=255)
cggcgTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAAt > 1:735268/1‑90 (MQ=255)
cggcgTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCt < 3:138618/130‑1 (MQ=255)
cggcgTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCt > 4:138618/1‑130 (MQ=255)
tCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTgg > 1:197694/1‑117 (MQ=255)
tCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTgg < 2:197694/117‑1 (MQ=255)
tGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTa > 2:718765/1‑146 (MQ=255)
tGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTa < 1:718765/146‑1 (MQ=255)
cGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTa > 4:529535/1‑139 (MQ=255)
cGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTa < 3:529535/139‑1 (MQ=255)
aagaaAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTaa < 1:562781/138‑1 (MQ=255)
aagaaAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTaa > 2:562781/1‑138 (MQ=255)
aagaaAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCAGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCagcgt > 2:824946/1‑148 (MQ=255)
tAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTg > 2:818816/1‑90 (MQ=255)
tAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTg < 1:818816/90‑1 (MQ=255)
aTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGt < 2:823823/124‑1 (MQ=255)
aTTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTAAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGt > 1:823823/1‑124 (MQ=255)
gtGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTg > 4:820193/2‑148 (MQ=255)
gTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTAt < 1:824946/148‑1 (MQ=255)
aaaaaTATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTaa > 3:758936/1‑86 (MQ=255)
aaaaaTATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTaa < 4:758936/86‑1 (MQ=255)
aaaTATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAAc > 2:472814/1‑74 (MQ=255)
aaaTATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAAc < 1:472814/74‑1 (MQ=255)
aCAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGa > 1:195437/1‑41 (MQ=255)
aCAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGa < 2:195437/41‑1 (MQ=255)
ggTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGt > 2:716974/1‑92 (MQ=255)
ggTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGt < 1:716974/92‑1 (MQ=255)
|
GAAAAGGGAATTAAAGGGATAAATAACGGCGAAATAGAGTGATCAAATAACGTCTGTTTATTAGCCAGCCAGCGGCGTTGGGTTCGTGATTAGCGAAGAAAAATCATCATAAATTGGTGAAAAATATAACAGGTAGTTAAAAACCATTAGTGCTGAGTAAATTGCCGGATGACATCAGAACGATGCCATCCGAACAGTGGCTTAACCCTGACGGTTGAAACGTTGCGTTTTAACGTCCAGCGTTAGCGTTTCTTCTGGTTGTAT > NC_000913/1247495‑1247758
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
