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 |
1,191,560 |
T→C |
68.4% |
*116W (TGA→TGG) |
rnd ← |
ribonuclease D |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,191,560 | 0 | T | C | 68.4%
| 46.0
/ 27.5
| 38 | *116W (TGA→TGG) | rnd | ribonuclease D |
| Reads supporting (aligned to +/- strand): ref base T (8/4); new base C (13/13); total (21/17) |
| Fisher's exact test for biased strand distribution p-value = 4.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCAGTCGGTGCGCGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGTAATTCGCCA > minE/1191491‑1191629
|
ccagTCGGTGCGCGATTCACTCTTGTCCAGCGTAACGCCTGAATACTCTTCCACCATGGAAGCGAAACCt > 1:1681126/1‑70 (MQ=255)
cagTCGGTGCGCGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCa < 1:1977452/71‑1 (MQ=255)
cagTCGGTGCGCGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCa < 1:3490703/71‑1 (MQ=255)
tGCGCGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATc < 1:3023157/71‑1 (MQ=255)
gcgcGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCg > 1:2542051/1‑71 (MQ=255)
aTTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCg > 1:2755065/1‑70 (MQ=255)
cACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCg > 1:1135184/1‑71 (MQ=255)
ctTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAg > 1:28781/1‑70 (MQ=255)
ttGTCCAGCGTAACGCCGGAATACTCTTCCACGATGGAAGCGAAACCCCATGACATCGGGCg < 1:2797028/62‑1 (MQ=255)
ttGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCg < 1:965766/62‑1 (MQ=255)
ttGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAg > 1:1124907/1‑69 (MQ=255)
gTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAgg > 1:779574/1‑71 (MQ=255)
gTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAgg > 1:3839902/1‑71 (MQ=255)
tCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATc < 1:3608321/54‑1 (MQ=255)
gCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGgcagc > 1:2531444/1‑70 (MQ=255)
cGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGgcagc > 1:121580/1‑69 (MQ=255)
tAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTc < 1:1886826/39‑1 (MQ=255)
tAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAgg < 1:180412/71‑1 (MQ=255)
aCGCCGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGAt > 1:1070834/1‑71 (MQ=255)
ccGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTg < 1:1597779/71‑1 (MQ=255)
cGGAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGc > 1:2454145/1‑71 (MQ=255)
ggAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCg < 1:3604656/71‑1 (MQ=255)
ggAATACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCg > 1:493544/1‑71 (MQ=255)
aaTACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCgtg < 1:1870589/71‑1 (MQ=255)
aaTACTCTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCgt > 1:1265140/1‑70 (MQ=255)
aaTACACTTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCgtg < 1:601231/71‑1 (MQ=255)
ctctTCCACCATGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGc > 1:1998379/1‑64 (MQ=255)
ttCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGtcaatc > 1:1852257/1‑70 (MQ=255)
ccaccaTGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGAtt > 1:3891556/1‑56 (MQ=255)
ccaccaTGGAAGCGAAACCCCATGACATCCGGCGTCCGCAGAAGGCAGCAAGGAtt > 1:2853789/1‑56 (MQ=255)
caTGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGtt > 1:2125496/1‑71 (MQ=255)
aTGGAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGGGTCAATCAAGGGTtg < 1:299214/71‑1 (MQ=255)
tGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTtgt < 1:483794/71‑1 (MQ=255)
gAAGCGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTtgtg < 1:373703/70‑1 (MQ=255)
aGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGt > 1:532097/1‑70 (MQ=255)
gCGAAACCCCATGACATCGGGCGTCCGCAGAAGgca > 1:1035836/1‑36 (MQ=255)
cGAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGTAAt < 1:1077240/71‑1 (MQ=255)
gAAACCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGt < 1:452368/67‑1 (MQ=255)
aaCCCCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGTAATTCg > 1:2510704/1‑71 (MQ=255)
tCATGACATCGGGCGTACGCAGAAGGCAGCAAGGATTTGAGTGTCAATCAAGGGTTGTGGTAATTCGCCa > 1:2205251/1‑70 (MQ=255)
|
CCAGTCGGTGCGCGATTCACTCTTGTCCAGCGTAACGCCGGAATACTCTTCCACCATGGAAGCGAAACCTCATGACATCGGGCGTCCGCAGAAGGCAGCAAGGATTTGCGTGTCAATCAAGGGTTGTGGTAATTCGCCA > minE/1191491‑1191629
|
| 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
