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 |
|
A16 F20 I0 R1
|
52 |
51.1 |
1736300 |
96.9% |
1682474 |
149.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP009273 |
3,856,737 |
G→A |
10.2% |
pseudogene (227/1617 nt) |
glvC ← |
pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP009273 | 3,856,737 | 0 | G | A | 10.2%
| 100.3
/ 3.3
| 39 | pseudogene (227/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| Reads supporting (aligned to +/- strand): ref base G (22/13); new base A (2/2); total (24/15) |
| Fisher's exact test for biased strand distribution p-value = 6.31e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.71e-01 |
GCGTCCTGAGTGAAATCGACGCCGAAGTAGCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGATGGCAAGAC > CP009273/3856602‑3856884
|
gcgTCCTGAGTGAAATCGACGCCGAAGTAGCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCCCGCCCCTGCGCTTGCTTAGCAAGGCCAAGGGGTAAACCAACAGc > 1:163986/1‑149 (MQ=255)
cGACGCCGAAGTAGCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGCAAGCAAAAATCAGCGGCata > 2:708802/1‑149 (MQ=255)
gCCGAAGTAGCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTCGCAAGGCCAATGGGTAAACACAAAGCAAAAATCCGCGGCATAttgc > 1:41292/1‑147 (MQ=255)
gCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGAGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCg > 2:862077/1‑149 (MQ=255)
gCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGAGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCg > 2:381226/1‑149 (MQ=255)
tCATTCACATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGccc > 1:503288/1‑149 (MQ=255)
cATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCct < 1:520044/149‑1 (MQ=255)
aTTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCctc > 2:85079/1‑149 (MQ=255)
cATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCaa < 1:833817/149‑1 (MQ=255)
gTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAAtgt < 1:856728/149‑1 (MQ=255)
gTTGATGAAATAGTTCCAGGGCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAAtgt < 1:412003/149‑1 (MQ=255)
aaaTAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCCCTTCAATAATGTTTACGAt > 1:749690/1‑149 (MQ=255)
aTAGTTCCAGGTCAGGAAACTCACCATCACCGACAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAACGGGTACACCGACAGCAAGAATCAGCAGCATATTCCGGACTACCGTCCAGCCGCCGTCTTCAATAATGTGTAGGAttt > 1:818054/1‑149 (MQ=255)
cAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATACGGTGTACGATTTGCGCGaa > 2:261479/1‑149 (MQ=255)
cAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTCCGATTTGCGCGaa > 2:351356/1‑149 (MQ=255)
cAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGaa < 2:180455/149‑1 (MQ=255)
tCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATaaa < 1:788400/149‑1 (MQ=255)
acccaccacCCCCCCCAGACAAGCACGCCCCTGCCCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCg < 1:27082/146‑1 (MQ=255)
ccATCACCGGTAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCg < 2:713574/149‑1 (MQ=255)
ccATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGGCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCg < 2:560283/149‑1 (MQ=255)
ccATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCCATACTGTGTACGATTTGCGCGAATAAACTGTTCGGATCg > 1:447060/1‑149 (MQ=255)
ccATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCg > 1:300535/1‑149 (MQ=255)
cGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGCGTGCTGCACGCGCGAATAAACTGTTCGGATCGGTCAGTg < 2:858785/149‑1 (MQ=255)
aCAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTCCGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTccc > 1:372480/1‑149 (MQ=255)
aCAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTccc > 2:800943/1‑149 (MQ=255)
aCAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAACGTGTACGATTTGCGCGAATAAACTGTTCGGGTCGGTCAGTGATTccc > 1:26739/1‑149 (MQ=255)
aGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGTCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGa < 2:565594/149‑1 (MQ=255)
cccTGCGCTTGCTTAGCAAGGCCCATGGGTAAACCGACAGCCAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACAt < 2:380935/149‑1 (MQ=255)
cTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACAACg > 1:560669/1‑149 (MQ=255)
cTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTAAGTGATTGGCCGACAAACATCg > 1:234848/1‑149 (MQ=255)
gcgcTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAGATCAGCGGCATATTACGGCATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCggg > 2:770783/1‑149 (MQ=255)
ttgcttAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGtttt > 2:187235/1‑149 (MQ=255)
cttAGCAAGGCCAATGAGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTgca < 1:862077/149‑1 (MQ=255)
cttAGCAAGGCCAATGAGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTgca < 1:381226/149‑1 (MQ=255)
aGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGAt > 2:630451/1‑149 (MQ=255)
ggCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTGCGTGGTTCCCCGACAAACATCGGGTGTTGCAGCAAGATg > 2:226415/1‑149 (MQ=255)
gCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGGTgg > 1:75607/1‑149 (MQ=255)
gCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGATgg > 1:124678/1‑149 (MQ=255)
tGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCCTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGATGGCAAGa < 2:503288/149‑1 (MQ=255)
gggTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGGAGCAAGATGGCAAGAc > 2:510222/1‑149 (MQ=255)
|
GCGTCCTGAGTGAAATCGACGCCGAAGTAGCTTCCCCAGGTCATTCCCATCGCGTTGATGAAATAGTTCCAGGTCAGGAAACTCACCATCACCGCCAGACAAGCACGCCCCTGCGCTTGCTTAGCAAGGCCAATGGGTAAACCGACAGCAAAAATCAGCGGCATATTACGGAATACCGTCCAACCGCCCTCTTCAATAATGTGTACGATTTGCGCGAATAAACTGTTCGGATCGGTCAGTGATTCCCCGACAAACATCGGGTTTTGCAGCAAGATGGCAAGAC > CP009273/3856602‑3856884
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
