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 |
497,197 |
C→T |
100% |
L96L (CTG→CTA) |
galT ← |
galactose‑1‑phosphate uridylyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 497,197 | 0 | C | T | 76.3%
| 21.0
/ 2.9
| 21 | L96L (CTG→CTA) | galT | galactose‑1‑phosphate uridylyltransferase |
| Reads supporting (aligned to +/- strand): ref base C (5/0); new base T (0/16); total (5/16) |
| Fisher's exact test for biased strand distribution p-value = 4.91e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TGATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGACTTTCTGGCGCATCTGGCGTGTCAGACATCAA > minE/497141‑497241
|
tgATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGa > 1:1120190/1‑69 (MQ=255)
tgATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGa > 1:3060973/1‑69 (MQ=255)
tgATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGa > 1:2838548/1‑69 (MQ=255)
tgATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGa > 1:2842387/1‑69 (MQ=255)
cAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGACTTTCTGGCGCATCt > 1:1848135/1‑69 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:980653/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:880239/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:419234/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:383390/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:3357383/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:3087093/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:2992331/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:2540377/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:2211808/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:1822525/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:1772464/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:1748420/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:167834/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:1478825/68‑1 (MQ=255)
accGCGCGCGCTCTGGCAACGCATTAGCGGATCGTG‑CTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:2435946/67‑1 (MQ=255)
gcTATGGCAACGCATTAGCGGATCGTTGCTTTCTGGCGCATCTGGCGTGTCAGACATCaa < 1:376855/60‑1 (MQ=255)
|
TGATCCGGTGAAAAGCAGATCACCCGGCTGGTGCCGCGCGCGCTCTGGCAACGCATCAGCGGATCGTGACTTTCTGGCGCATCTGGCGTGTCAGACATCAA > minE/497141‑497241
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
