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 |
1,259,163 |
A→C |
54.9% |
T587T (ACT→ACG) |
torZ ← |
trimethylamine N‑oxide reductase system III, catalytic subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,259,163 | 0 | A | C | 54.9%
| 20.8
/ 61.4
| 62 | T587T (ACT→ACG) | torZ | trimethylamine N‑oxide reductase system III, catalytic subunit |
| Reads supporting (aligned to +/- strand): ref base A (4/24); new base C (28/6); total (32/30) |
| Fisher's exact test for biased strand distribution p-value = 1.03e-07 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01 |
CGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTC > minE/1259096‑1259228
|
cgttcTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATa > 1:3338793/1‑68 (MQ=255)
cgttcTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATa > 1:1230043/1‑68 (MQ=255)
ttcttcTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGt < 1:1003041/68‑1 (MQ=255)
ttcttcTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGt < 1:564922/68‑1 (MQ=255)
ttcttcTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGt < 1:1319916/68‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:1793692/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:2073609/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:240071/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:1549767/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:256967/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:132478/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:2583193/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:1306552/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:310527/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:344909/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:369617/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:113793/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTgcg < 1:749548/69‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:3152210/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:2577489/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:2248005/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:1829033/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:1013212/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:1193532/67‑1 (MQ=255)
tgtgGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTg < 1:1308460/67‑1 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCa > 1:383715/1‑66 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:1247619/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:997005/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:3290177/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:3185043/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:2732996/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:26685/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:2651452/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:1565629/1‑68 (MQ=255)
cgcATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACg > 1:2316427/1‑68 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTgcgc > 1:3215136/1‑59 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCAcc > 1:1287253/1‑68 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCAcc > 1:3215139/1‑68 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1709657/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:378268/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:401612/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1207930/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:51956/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1217421/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1155103/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:3214302/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1658017/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:649823/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1131814/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:871249/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:910305/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1965783/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATCGTCACGCGTTGCGCACGCGCACCt > 1:1396320/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:1467260/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:16974/1‑69 (MQ=255)
tCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCt > 1:3404045/1‑69 (MQ=255)
tATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCg > 1:2287713/1‑68 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:2173266/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:3105383/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:738051/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:310206/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:3031293/69‑1 (MQ=255)
ggCATCGTCACGCGTTGCGCACGCGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCAtt < 1:2747374/69‑1 (MQ=255)
aTAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTc < 1:2164641/68‑1 (MQ=255)
|
CGTTCTTCTCGCTGTGGCGCATTTCGATCAGTTTATTTTGCTGCCAGAAGGCATTAAACATTGGCATAGTGACGCGTTGCGCACGGGCACCTTTCTGAGCGGCATCATAGAAAAATTTCAGCCACGCCATTTC > minE/1259096‑1259228
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
