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 |
2,664,355 |
A→G |
100% |
S37G (AGC→GGC) |
rtcA → |
RNA 3'‑terminal phosphate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,664,355 | 0 | A | G | 80.1%
| 24.2
/ 1.1
| 20 | S37G (AGC→GGC) | rtcA | RNA 3'‑terminal phosphate cyclase |
| Reads supporting (aligned to +/- strand): ref base A (0/4); new base G (16/0); total (16/4) |
| Fisher's exact test for biased strand distribution p-value = 2.06e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTG > minE/2664296‑2664402
|
aGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCAt > 1:1403948/1‑64 (MQ=255)
aGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCAt > 1:14055/1‑64 (MQ=255)
aGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCAt > 1:1512875/1‑64 (MQ=255)
aGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCAt > 1:166541/1‑64 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCa > 1:2285659/1‑39 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTg > 1:1230614/1‑45 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCgggg > 1:1992462/1‑65 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:1320667/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:415052/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:344147/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:2844531/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:2701348/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:2501493/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:2481334/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:2232406/1‑66 (MQ=255)
tGTCGATGATAACCGGCCAGCCATTTACCATCACCGGCATTCGTGCCGGGCGGGCGAAACCGGGGc > 1:138813/1‑66 (MQ=255)
ggCCAGCCATTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTg < 1:1452206/69‑1 (MQ=255)
ggCCAGCCATTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTg < 1:657785/69‑1 (MQ=255)
gccagccaTTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTg < 1:1349906/68‑1 (MQ=255)
gccagccaTTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTg < 1:876613/68‑1 (MQ=255)
|
AGATCCTGCGCTCGGCGCTGAGCCTGTCGATGATAACCGGCCAGCCATTTACCATCACCAGCATTCGTGCCGGGCGGGCGAAACCGGGGCTGTTGCGCCAGCATCTG > minE/2664296‑2664402
|
| 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
