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 |
1,657,763 |
T→C |
33.3% |
Y678Y (TAT→TAC) |
ppk → |
polyphosphate kinase, component of RNA degradosome |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,657,763 | 0 | T | C | 33.3%
| 38.2
/ 27.4
| 54 | Y678Y (TAT→TAC) | ppk | polyphosphate kinase, component of RNA degradosome |
| Reads supporting (aligned to +/- strand): ref base T (13/23); new base C (8/10); total (21/33) |
| Fisher's exact test for biased strand distribution p-value = 5.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAAGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATCCCCTCGTC > minE/1657695‑1657828
|
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTTGCGATTTAt < 1:2394813/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:469343/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:2146006/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:1699587/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:506475/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:2703692/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:3134071/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:3280793/69‑1 (MQ=255)
aaaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:3406157/69‑1 (MQ=255)
aaGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTAt < 1:1832831/68‑1 (MQ=255)
tCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaaca < 1:2723603/69‑1 (MQ=255)
tCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaaca < 1:83372/69‑1 (MQ=255)
tCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaaca < 1:526833/69‑1 (MQ=255)
ccccGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaacaa < 1:129719/69‑1 (MQ=255)
ccccGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaacaa < 1:2842271/69‑1 (MQ=255)
ccccGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaacaa < 1:450173/69‑1 (MQ=255)
gCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGaaca < 1:810149/61‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:3182708/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:1004/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:3274065/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:2564504/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:1214108/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:128395/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:962748/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:1591926/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:164154/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:1929319/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:1653724/69‑1 (MQ=255)
cgccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAAccc < 1:738982/69‑1 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:2017424/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:1515356/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:2659211/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:2524963/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:243363/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:2357397/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:2069128/1‑69 (MQ=255)
gccgcAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCt > 1:563390/1‑69 (MQ=255)
aGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCaa < 1:3332082/69‑1 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAAc > 1:735533/1‑46 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAAt > 1:2345523/1‑68 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAAt > 1:3180410/1‑68 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATc > 1:1630093/1‑69 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATc > 1:141558/1‑69 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATc > 1:2048388/1‑69 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATc > 1:3342183/1‑69 (MQ=255)
ttGGCGATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATc > 1:1725961/1‑69 (MQ=255)
tGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATcc > 1:2802205/1‑69 (MQ=255)
tGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATcc > 1:2819703/1‑69 (MQ=255)
tGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATcc > 1:1261082/1‑69 (MQ=255)
ggCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATccc < 1:683416/69‑1 (MQ=255)
ggCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATccc < 1:3121038/69‑1 (MQ=255)
cGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATccc < 1:3186869/67‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:1110479/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:367643/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:2747951/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:263074/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:2303623/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:1700740/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:1695473/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:118958/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACCCTATGCCAATACACGATAAATCCCCt < 1:118082/68‑1 (MQ=255)
gATTTACGACTACATCAAATCACTCGAACAATCTGAATAACACTATGCCAATACACGATAAATCCCCt < 1:2041565/68‑1 (MQ=255)
ttATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATCCCCTCGTc > 1:2541728/1‑69 (MQ=255)
ttATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATCCCCTCGTc > 1:1996592/1‑69 (MQ=255)
|
AAAGAACTCAGTAATCGCTACGTTCCCCGCGGCAATCGCCGCAAAGTACGGGCGCAGTTGGCGATTTATGACTACATCAAATCACTCGAACAACCTGAATAACCCTATGCCAATACACGATAAATCCCCTCGTC > minE/1657695‑1657828
|
| 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
