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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
837,040 |
T→C |
12.0% |
L75L (TTG→CTG) |
narJ → |
molybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 837,040 | 0 | T | C | 12.0%
| 127.5
/ 8.9
| 50 | L75L (TTG→CTG) | narJ | molybdenum‑cofactor‑assembly chaperone subunit (delta subunit) of nitrate reductase 1 |
| Reads supporting (aligned to +/- strand): ref base T (23/21); new base C (3/3); total (26/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.05e-01 |
GACGATGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTG > minE/836970‑837102
|
gacgaTGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGt < 1:3372245/71‑1 (MQ=255)
cgaTGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTg < 1:620315/71‑1 (MQ=255)
cgaTGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTg > 1:3121504/1‑71 (MQ=255)
gaTGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACCTCACTGTTGc > 1:60627/1‑71 (MQ=255)
ggATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCTCGCCACGTCACTGTTGCTGt > 1:2692760/1‑71 (MQ=255)
ggATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGt > 1:2537115/1‑71 (MQ=255)
gATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGtt < 1:3213275/71‑1 (MQ=255)
ccGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTg > 1:3041469/1‑70 (MQ=255)
ccGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTg > 1:2394300/1‑70 (MQ=255)
cGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTg > 1:1366829/1‑69 (MQ=255)
cGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGaa < 1:3822977/71‑1 (MQ=255)
cTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACa > 1:1587823/1‑71 (MQ=255)
tCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACAt > 1:1078563/1‑71 (MQ=255)
gATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACAtgt > 1:332109/1‑71 (MQ=255)
gATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACAtg < 1:1482210/70‑1 (MQ=255)
gATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACAt < 1:2832612/69‑1 (MQ=255)
gATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACAt < 1:523840/69‑1 (MQ=255)
gCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCa > 1:2484570/1‑71 (MQ=255)
cccAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGaa > 1:398854/1‑62 (MQ=255)
ggCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGc > 1:850909/1‑70 (MQ=255)
ggCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg < 1:953802/71‑1 (MQ=255)
ggCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCg < 1:3080495/71‑1 (MQ=255)
gcgcAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGa < 1:2542945/71‑1 (MQ=255)
cgcAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGaa < 1:3502846/71‑1 (MQ=255)
aCAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGtt > 1:2431471/1‑40 (MQ=255)
aCAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCcgc > 1:859730/1‑71 (MQ=255)
aGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGaa < 1:3395378/63‑1 (MQ=255)
agAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGAcc > 1:3444475/2‑71 (MQ=255)
gAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGAcc > 1:1583246/1‑70 (MQ=255)
gAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACcg < 1:1256061/71‑1 (MQ=255)
gAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACcg < 1:2717555/71‑1 (MQ=255)
gAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACcg > 1:2089670/1‑71 (MQ=255)
aCTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACa > 1:1874213/1‑45 (MQ=255)
ttCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGcc < 1:1099489/70‑1 (MQ=255)
ttCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGc > 1:1050852/1‑69 (MQ=255)
ttCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCa < 1:1531943/71‑1 (MQ=255)
cGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGa < 1:3029579/51‑1 (MQ=255)
aCCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGc > 1:2398564/1‑70 (MQ=255)
gTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtg < 1:2108400/71‑1 (MQ=255)
gggcgcaCCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggt < 1:874864/68‑1 (MQ=255)
cgcaCCACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGa < 1:2391791/71‑1 (MQ=255)
accACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACct > 1:1722484/2‑71 (MQ=255)
accACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACct > 1:3603164/2‑71 (MQ=255)
ccACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGc < 1:3107988/58‑1 (MQ=255)
cACGTCGCTGCTGCTGTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAATGGTGGACctgc > 1:1785592/1‑71 (MQ=255)
cACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc > 1:2225904/1‑71 (MQ=255)
cACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc > 1:2221230/1‑71 (MQ=255)
cACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgc < 1:1465211/71‑1 (MQ=255)
cGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggtg < 1:1637635/62‑1 (MQ=255)
gctgctgctgTTCGAACATGTTCATGCCGAGTCCCGCGATCGCGGCCAGGCAAtggt > 1:1731759/2‑57 (MQ=255)
aCTGTTGCTGTTTGAACATGTGCACGGCTAATCCCGCGACCGCGGCCAGGCGATGGTGGACctgctg < 1:2037465/67‑1 (MQ=255)
tGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGAtggt < 1:2800032/55‑1 (MQ=255)
tGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGAcc > 1:1267926/1‑60 (MQ=255)
|
GACGATGGATCCGCTCGATGCCCAGGCGCAGTACAGCGAACTGTTCGACCGTGGCCGCGCCACGTCACTGTTGCTGTTTGAACATGTGCACGGCGAATCCCGCGACCGCGGCCAGGCGATGGTGGACCTGCTG > minE/836970‑837102
|
| 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
