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 |
305,631 |
A→G |
29.3% |
L486L (TTA→CTA) |
ylaB ← |
conserved inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 305,631 | 0 | A | G | 29.3%
| 46.4
/ 20.8
| 51 | L486L (TTA→CTA) | ylaB | conserved inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (20/16); new base G (8/7); total (28/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.22e-01 |
CTTCTTTCGGTAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGTTTTTGC > minE/305568‑305694
|
cttcttTCGGTAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCAct < 1:2166835/69‑1 (MQ=255)
tAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGtt < 1:841474/68‑1 (MQ=255)
tAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGtt < 1:487198/68‑1 (MQ=255)
tAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGtt < 1:1831614/68‑1 (MQ=255)
tAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGtt < 1:1768467/68‑1 (MQ=255)
aTGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGtt < 1:1282332/66‑1 (MQ=255)
gCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACt < 1:53931/68‑1 (MQ=255)
gagCCAGCCCTGACCTTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTGCTGGTTTCGATTcc > 1:652243/1‑69 (MQ=255)
gagCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTg > 1:603843/1‑51 (MQ=255)
gagCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTc > 1:2138773/1‑68 (MQ=255)
cTGACCGTATTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:3148729/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCCCtcttc > 1:1773094/1‑39 (MQ=38)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:2924216/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:2966415/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:2912347/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:2161522/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:1220124/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAGCCACTCTTCTTg > 1:1918202/1‑42 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:1980855/69‑1 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:3235584/69‑1 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:1507032/69‑1 (MQ=255)
cTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:1735384/69‑1 (MQ=255)
tGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAcc < 1:3422195/69‑1 (MQ=255)
tGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAcc < 1:3231669/69‑1 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:1497452/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:1142618/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:689883/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:665913/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:1254055/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:479851/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:2722562/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:2479950/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:1993129/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:2222332/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTTTACTGGATTCGATTCCCTCCGCTACCATTTTCAGTTTCAgtg > 1:345308/1‑69 (MQ=255)
cATGCTGGCGTAACCACTCTTCTTGTATACTGGTTTCGATTCCCTCCGCTACCATtttcagtttcag > 1:3191071/1‑67 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:2589240/48‑1 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGtttt > 1:2616234/1‑69 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGtttt > 1:2102049/1‑69 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGtttt > 1:2270609/1‑69 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGtttt > 1:472973/1‑69 (MQ=255)
cTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGtttt > 1:1412563/1‑69 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:2647797/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:786875/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:1947034/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:1423618/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:1484134/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:3412856/68‑1 (MQ=255)
ggCGTAGCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCAACCATTTTCAGTTTCAGTGttttt < 1:2643830/68‑1 (MQ=255)
gTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGTTTTTGc < 1:657137/67‑1 (MQ=255)
gTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGTTTTTGc < 1:2155236/67‑1 (MQ=255)
aCCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTAc < 1:2116018/40‑1 (MQ=255)
|
CTTCTTTCGGTAATGCCTTGCTGTAGAGCCAGCCCTGACCGTAGTGCACGCCATGCTGGCGTAACCACTCTTCTTGTTTACTGGTTTCGATTCCCTCCGCTACCATTTTCAGTTTCAGTGTTTTTGC > minE/305568‑305694
|
| 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
