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 |
1,139,074 |
T→C |
41.1% |
I150I (ATT→ATC) |
ydjN → |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,139,074 | 0 | T | C | 41.1%
| 16.5
/ 40.0
| 56 | I150I (ATT→ATC) | ydjN | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (11/22); new base C (4/19); total (15/41) |
| Fisher's exact test for biased strand distribution p-value = 2.31e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGGTTTGACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTCCTTTATC > minE/1139014‑1139137
|
tggtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTa > 1:1859461/1‑68 (MQ=255)
gtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:1448902/68‑1 (MQ=255)
gtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:778834/68‑1 (MQ=255)
gtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:378762/68‑1 (MQ=255)
gtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:2980270/68‑1 (MQ=255)
gtttgACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:1750247/68‑1 (MQ=255)
tCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATCGa > 1:1971931/1‑45 (MQ=255)
tCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATCGa > 1:2232487/1‑45 (MQ=255)
tCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATCGa > 1:3434286/1‑45 (MQ=255)
tCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATCGa > 1:2633232/1‑45 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:98958/1‑69 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:2210782/1‑69 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:222398/1‑69 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:2919342/1‑69 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:1566592/1‑69 (MQ=255)
cTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTctct > 1:1486051/1‑69 (MQ=255)
tggtgCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGt < 1:2699165/69‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAAc < 1:130349/35‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGc < 1:2762186/69‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGc < 1:808278/69‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGc < 1:2026461/69‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGc < 1:2064404/69‑1 (MQ=255)
cAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGGTGGTAAAGTCTCTGATCTGAGCGTTCCGc < 1:1888312/69‑1 (MQ=255)
aaaCTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCa < 1:1870010/67‑1 (MQ=255)
tGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGt < 1:2217776/69‑1 (MQ=255)
cGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTg > 1:958946/1‑69 (MQ=255)
cGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTg > 1:2498188/1‑69 (MQ=255)
cGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTg > 1:2915462/1‑69 (MQ=255)
cGTCTGAACGCCATTGAAAGTAACTATGATGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTg > 1:1679078/1‑69 (MQ=255)
cTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTcc < 1:838166/69‑1 (MQ=255)
cTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTcc < 1:2671515/69‑1 (MQ=255)
cTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTcc < 1:617649/69‑1 (MQ=255)
cTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTcc < 1:1712736/69‑1 (MQ=255)
cTGAACGCCATTGAAAGTAACTATGTTGCTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTcc < 1:1922384/69‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTTGTc < 1:1437181/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1643559/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1243886/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1503442/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:380473/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:432462/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1477596/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:834544/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:2029602/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:3055323/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:3041909/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:298778/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:2683455/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1845182/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:2491154/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1969363/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1048853/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:1979915/62‑1 (MQ=255)
tGAACGCCATCGAAAGTAACTATGTTGGTAAAGTCTCTGACCTGAGCGTTCCGCAGCTGGTc < 1:2100443/62‑1 (MQ=255)
gCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTCCTTTATc < 1:1809412/69‑1 (MQ=255)
gCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTCCTTTATc < 1:734984/69‑1 (MQ=255)
cATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTCCTTTATc < 1:1755790/67‑1 (MQ=255)
|
TGGTTTGACGGCTGAAGGTCTGGTTCAGGGTGGTGCAGAAACTGCACGTCTGAACGCCATTGAAAGTAACTATGTTGGTAAAGTCTCTGATCTGAGCGTTCCGCAGCTGGTCTTGTCCTTTATC > minE/1139014‑1139137
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
