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 |
906,069 |
T→C |
100% |
I32I (ATT→ATC) |
ycjR → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 906,069 | 0 | T | C | 85.6%
| 69.4
/ 2.6
| 42 | I32I (ATT→ATC) | ycjR | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (0/6); new base C (0/35); total (0/42) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATATCAAAGAGATGGGCTTCGATGGTTTTGAGATTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTA > minE/906035‑906132
|
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATGGACGGCAAACTGCTGGtca < 1:43684/54‑3 (MQ=255)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:249831/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:818231/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:731753/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:706981/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:637915/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:510696/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:487510/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:454484/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:3368781/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:3104272/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:269007/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1018864/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2448267/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2304468/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2286725/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2157578/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1538268/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1715942/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1793638/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1838137/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:185226/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1248523/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1087332/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:1895740/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2174353/54‑3 (MQ=38)
atatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:205571/54‑3 (MQ=38)
tatCAAAGAGATGGGTTTCGATGGTTTTGAGATCGACGGCAAACTGCTGGtca < 1:2500220/53‑3 (MQ=38)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:255387/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:2984994/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:3426852/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:350953/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:2381443/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:441063/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGCAGCAATCAAAGa < 1:149922/68‑1 (MQ=255)
gATGGTTTTGAGATCGACGGCAAACTGCTGGTCAACAATCTCGAAGAAGTCAAAGAAGCAATCAAAGa < 1:1985041/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:1435484/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:1041213/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:3324551/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:3051267/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:2756098/68‑1 (MQ=255)
agaTTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTa < 1:1920486/68‑1 (MQ=255)
|
ATATCAAAGAGATGGGCTTCGATGGTTTTGAGATTGACGGCAAACTGCTGGTTAACAACATCGAAGAAGTCAAAGCGGCGATCAAAGAAACCGGTTTA > minE/906035‑906132
|
| 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
