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 |
740,625 |
C→T |
43.9% |
S61N (AGC→AAC) |
fhuE ← |
ferric‑rhodotorulic acid outer membrane transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 740,625 | 0 | C | T | 43.9%
| 11.9
/ 35.4
| 50 | S61N (AGC→AAC) | fhuE | ferric‑rhodotorulic acid outer membrane transporter |
| Reads supporting (aligned to +/- strand): ref base C (25/3); new base T (4/18); total (29/21) |
| Fisher's exact test for biased strand distribution p-value = 3.82e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
GTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAG > minE/740559‑740688
|
gTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCt > 1:1272452/1‑68 (MQ=255)
gTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCt > 1:426427/1‑68 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCAtt > 1:842560/1‑59 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:1129668/1‑69 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:2327669/1‑69 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:2336102/1‑69 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:3383810/1‑69 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:1296811/1‑69 (MQ=255)
tCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCcatca > 1:96843/1‑69 (MQ=255)
cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat > 1:1522627/1‑69 (MQ=255)
cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat > 1:2578302/1‑69 (MQ=255)
cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat > 1:1851978/1‑69 (MQ=255)
cACGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTCGCcatcat > 1:498142/1‑69 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2817377/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2457302/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2452634/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2951010/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:242033/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2893267/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:216792/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:559543/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:1919548/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:714515/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:173592/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:775302/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:803712/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:148533/60‑1 (MQ=255)
aCGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:1393703/60‑1 (MQ=255)
aCGTTGAGTCATCCGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:3183835/60‑1 (MQ=255)
cGTTGAGTCATCTGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:2398404/59‑1 (MQ=255)
gTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGc < 1:991480/68‑1 (MQ=255)
cATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCtgt < 1:2685292/69‑1 (MQ=255)
cATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCtgt < 1:540980/69‑1 (MQ=255)
tGCATTTTTGTACCCGCAGAGGTAGACGTTACGTTGTAATCATTTTc < 1:296950/47‑1 (MQ=255)
aGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTttc > 1:113902/1‑69 (MQ=255)
aGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTttc > 1:2061834/1‑69 (MQ=255)
gACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTg > 1:2361000/1‑46 (MQ=255)
gACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGa > 1:498810/1‑47 (MQ=255)
gACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGa > 1:1756946/1‑47 (MQ=255)
gACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGa > 1:1475011/1‑47 (MQ=255)
gACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGa > 1:1253424/1‑47 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAAcc > 1:2420823/1‑46 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTcaacaa > 1:2014844/1‑54 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:419868/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:583026/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:759087/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:171742/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:1667502/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAg > 1:2869591/1‑69 (MQ=255)
ttACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAAACACCGTTTCTTCAg > 1:824540/1‑69 (MQ=255)
|
GTGACCGACTGAGGAATATCACGTTGAGTCATCTGCATTTTGGTACCCGCAGAGGTAGACGTTACGCTGTAATCATTTTCGCCATCATCTGGAGCTGTGGCTGAACCCTCAACAATCACCGTTTCTTCAG > minE/740559‑740688
|
| 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
