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 |
2,969,931 |
G→A |
78.9% |
L159L (CTC→CTT) |
lplA ← |
lipoate‑protein ligase A |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,969,931 | 0 | G | A | 78.9%
| 62.2
/ 10.3
| 47 | L159L (CTC→CTT) | lplA | lipoate‑protein ligase A |
| Reads supporting (aligned to +/- strand): ref base G (7/3); new base A (3/34); total (10/37) |
| Fisher's exact test for biased strand distribution p-value = 1.86e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
GACGTAATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCTTTGGTTTC > minE/2969869‑2969984
|
gACGTAATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTc > 1:3214264/1‑68 (MQ=255)
aTGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTg > 1:2667792/1‑69 (MQ=255)
aTGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTg > 1:2746819/1‑69 (MQ=255)
aTGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTg > 1:3087400/1‑69 (MQ=255)
aTGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTAAGGTCGGCATTg > 1:2598989/1‑69 (MQ=255)
gCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGa < 1:156920/68‑1 (MQ=255)
gCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGa < 1:835428/68‑1 (MQ=255)
gccgccAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCaa < 1:2740529/68‑1 (MQ=255)
ttCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCgtgg > 1:3344588/1‑69 (MQ=255)
ttCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCgtgg > 1:1102026/1‑69 (MQ=255)
ttCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCgtgg > 1:2586509/1‑69 (MQ=255)
tCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCgtgg > 1:624/1‑68 (MQ=255)
tCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCgtgg > 1:723363/1‑68 (MQ=255)
gaTATTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:2718499/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:2983575/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:533158/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:419631/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:3333492/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:1057657/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:66769/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:686444/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:1558675/52‑1 (MQ=255)
gaTAGTTTGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:1473787/52‑1 (MQ=255)
gaTAGTTTACCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCgtggtg < 1:488089/52‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACTATCTTTGGTTTc < 1:480345/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:86341/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:398641/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:102584/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:991600/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:372041/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:3396216/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:3395238/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:3392311/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:3110873/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:3080605/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2935856/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2935475/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2908023/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2767717/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2724436/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2336851/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2289752/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:2101956/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:1569322/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:1253036/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTCGGCATTGAGCAGCAAAGGGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:462480/66‑1 (MQ=255)
tGCCAGGCGGCTAAGGTAGGCATTGAGCAGCAAAGTGCCGTGGTGGAAGCCACGATCTTTGGTTTc < 1:895194/66‑1 (MQ=255)
|
GACGTAATGCCTTTCGCCGCCAGTTTCTTTTTATCCGGATTGAGATAGTTTGCCAGGCGGCTGAGGTCGGCATTGAGTAGCAAGGTGCCGTGGTGGAAGCCGCGATCTTTGGTTTC > minE/2969869‑2969984
|
| 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
