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 |
451,502 |
G→A |
29.6% |
L178L (CTA→TTA) |
kdpA ← |
potassium translocating ATPase, subunit A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 451,502 | 0 | G | A | 29.6%
| 73.9
/ 31.1
| 74 | L178L (CTA→TTA) | kdpA | potassium translocating ATPase, subunit A |
| Reads supporting (aligned to +/- strand): ref base G (29/23); new base A (13/9); total (42/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01 |
GCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATG > minE/451436‑451557
|
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg < 1:2479046/67‑1 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg < 1:2846916/67‑1 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg < 1:2882688/67‑1 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg < 1:3046805/67‑1 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:1982245/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:2059857/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:2636659/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:1682277/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:152871/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:418051/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:602376/1‑69 (MQ=255)
gCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCa > 1:774006/1‑69 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:3301808/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:4566/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:571336/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:577268/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:719768/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:2393143/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:2374971/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:218266/69‑1 (MQ=255)
gTTTTGCAGCGCACCTTGTTGTATAAAAAACAGTGCGATCAACAATGCCACAGGGGCTAACACCCATaa < 1:1102223/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAg < 1:1739659/45‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:1576099/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:2565175/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:2966468/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:633449/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:656512/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:1191916/69‑1 (MQ=255)
ttgttgAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:744943/69‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:2107227/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:649172/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:2221332/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:623687/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:1216571/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:3275991/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:1668383/54‑1 (MQ=255)
cAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAg < 1:2748974/54‑1 (MQ=255)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:469492/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:1615103/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:2930619/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:401818/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:474377/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:2763259/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:5295/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:1718880/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:539216/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:1283635/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:810623/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:1853756/3‑44 (MQ=37)
cgaTCAACAATGCCACAGGGGCTAACACCCATAACGTGATGCGt > 1:833154/3‑44 (MQ=37)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1290962/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1012912/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1309414/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1334428/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:988059/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1839605/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:3029395/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:161906/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:2329595/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:2004867/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:2551851/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:2093905/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGt > 1:1828999/1‑37 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCg > 1:3311202/1‑53 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa > 1:2117784/1‑69 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa > 1:2184529/1‑69 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa > 1:1839305/1‑69 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa > 1:268060/1‑69 (MQ=255)
cAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGa > 1:3286042/1‑69 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:2077977/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:896898/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:756283/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:3404993/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:2165281/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:241636/69‑1 (MQ=255)
caacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:3412743/69‑1 (MQ=255)
aacGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCt < 1:571078/68‑1 (MQ=255)
aCTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATg > 1:2584139/1‑60 (MQ=255)
aCTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATg > 1:9688/1‑60 (MQ=255)
gCACCCATAACGTGATGCGTAGCAGAGCGACCCAGGCATTCCCGAGCGTGCt < 1:1869859/52‑1 (MQ=255)
|
GCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATG > minE/451436‑451557
|
| 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
