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 |
1,980,200 |
C→T |
55.3% |
P90P (CCC→CCT) |
yqgE → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,980,200 | 0 | C | T | 55.3%
| 5.2
/ 35.7
| 47 | P90P (CCC→CCT) | yqgE | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (3/18); new base T (22/4); total (25/22) |
| Fisher's exact test for biased strand distribution p-value = 1.47e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.19e-01 |
GTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCCGCGATGTGC > minE/1980144‑1980264
|
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCTTCCAATTTTGCt < 1:3224935/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCTTCCAATTTTGCt < 1:2221642/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCTTCCAATTTTGCt < 1:2739073/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCTTCCAATTTTGCt < 1:3175722/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCt < 1:3135830/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCt < 1:1540866/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCt < 1:421224/69‑1 (MQ=255)
gTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCt < 1:2103726/69‑1 (MQ=255)
cggTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCg < 1:2694490/69‑1 (MQ=255)
tgAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGacaa < 1:3144458/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:1864397/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:2753680/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:298272/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:3026031/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:2387807/69‑1 (MQ=255)
tCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGt < 1:3297138/69‑1 (MQ=255)
cgcgGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTa < 1:755182/69‑1 (MQ=255)
cgcgGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTa < 1:137991/69‑1 (MQ=255)
ttGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACTGTAATGACCACTTcc > 1:2864454/1‑69 (MQ=255)
ttGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTcc > 1:696428/1‑69 (MQ=255)
tACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCcgcg < 1:1901890/68‑1 (MQ=255)
tACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCcgcg < 1:132361/68‑1 (MQ=255)
cTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCC‑CGAtgt > 1:1673650/1‑69 (MQ=255)
ccGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCCGCGAtgt < 1:859926/68‑1 (MQ=255)
ccGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCCGCGAtgt < 1:160759/68‑1 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGAtgtg > 1:1718099/1‑68 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGAtgtcc > 1:1801677/1‑67 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:3272241/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:3417021/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:421353/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:496766/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:617927/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:808339/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:241460/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2781838/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2541004/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:110331/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2396669/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2372841/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2206247/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2172154/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:2067335/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:1810766/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:1800875/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:1348871/1‑69 (MQ=255)
cGCCTTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATGACCACTTCCCGCGATGTGc > 1:1157063/1‑69 (MQ=255)
cGCCTTCCAATATTGCTTCCAGCATTCGCATTTCAGACAACACAGTGATCACCACTTCCCGCGATGTGc > 1:2059495/1‑69 (MQ=255)
|
GTTATGCTCGGCGGTCCGCTGGCTGAAGATCGCGGGTTTATTTTGCATACTCCGCCCTCCAATTTTGCTTCCAGCATTCGCATTTCAGACAACACGGTAATGACCACTTCCCGCGATGTGC > minE/1980144‑1980264
|
| 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
