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 |
|
A3 F1 I1 R1
|
57 |
49.8 |
2216334 |
94.8% |
2101084 |
113.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,335,018 |
G→A |
L543L (CTG→TTG) |
yfaA ← |
DUF2138 family protein, putative host defense protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,335,018 | 0 | G | A | 97.8%
| 156.9
/ ‑3.5
| 46 | coding (1627/1689 nt) | yfaA | DUF2138 family protein, putative host defense protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (21/24); minor base . (1/0); total (22/24) |
| Fisher's exact test for biased strand distribution p-value = 4.78e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.08e-01 |
CATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAGCTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTA > NC_000913/2334890‑2335152
|
cATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACa > 2:498817/1‑139 (MQ=255)
tCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATaa > 1:666546/1‑139 (MQ=255)
aGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAAcg < 1:221724/139‑1 (MQ=255)
aGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAAcg < 1:454006/139‑1 (MQ=255)
cATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAAcgcg < 2:867946/139‑1 (MQ=255)
aTTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCgg < 2:181665/139‑1 (MQ=255)
aacaacACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAg > 2:892371/1‑139 (MQ=255)
acacaacacaGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTc < 1:892371/139‑1 (MQ=255)
agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCa < 2:665190/99‑1 (MQ=255)
agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCa > 1:665190/1‑99 (MQ=255)
agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg < 2:796471/139‑1 (MQ=255)
agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg > 2:742706/1‑139 (MQ=255)
agccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg > 2:1086632/1‑139 (MQ=255)
ccagcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCa < 1:1038196/139‑1 (MQ=255)
gcAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATta > 2:330123/1‑139 (MQ=255)
cccGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGt > 2:541102/1‑139 (MQ=255)
gCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTc > 2:328080/1‑139 (MQ=255)
tGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCga < 1:189797/139‑1 (MQ=255)
gCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCgag > 1:152112/1‑139 (MQ=255)
ccAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCgaga < 1:330123/139‑1 (MQ=255)
aGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGACATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGAtt < 1:481313/139‑1 (MQ=255)
ggTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCa < 2:418988/139‑1 (MQ=255)
ccACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTg > 1:485021/1‑139 (MQ=255)
aCTGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAATCCGGTTCGAGATTCTTCGGCAGACTGGt < 2:197786/139‑1 (MQ=255)
tGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg < 1:630714/77‑1 (MQ=255)
tGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCgg > 2:630714/1‑77 (MQ=255)
tGCCAGGCGGCACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCa > 1:511145/1‑139 (MQ=255)
gcggcACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTgcg < 2:823653/90‑1 (MQ=255)
gcggcACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTgcg > 1:823653/1‑90 (MQ=255)
cACCGGGTTCCATCTGGGCCAACTTCATGGCATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGtt > 2:844130/1‑139 (MQ=255)
cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCt < 2:497841/63‑1 (MQ=255)
cACCGGGTTCCATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCt > 1:497841/1‑63 (MQ=255)
aCCGGGTTCCATCTGGGCCAACTTCATGACATAAcgcg < 2:310659/38‑1 (MQ=255)
aCCGGGTTCCATCTGGGCCAACTTCATGACATAAcgcg > 1:310659/1‑38 (MQ=255)
ccGGGTTCCATCTGGGCCA‑CTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACg > 1:844908/1‑139 (MQ=255)
ccATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGcagcag < 2:943241/139‑1 (MQ=255)
cATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGt < 1:328080/139‑1 (MQ=255)
cATCTGGGCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGt < 2:485021/139‑1 (MQ=255)
gggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACgca > 2:628663/1‑129 (MQ=255)
gggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACgca < 1:628663/129‑1 (MQ=255)
ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTc > 2:1039993/1‑42 (MQ=255)
ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTc < 1:1039993/42‑1 (MQ=255)
ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGt < 2:1031126/133‑1 (MQ=255)
ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGt > 1:1031126/1‑133 (MQ=255)
ggCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCt > 2:32023/1‑139 (MQ=255)
gCCAACTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTa < 2:225458/139‑1 (MQ=255)
|
CATTCAGCATTTCGCTATGGGCAACAACACAACACAGCCAGCAAATCAGCGCCAGCAGCCCGTGCCTCATAGCGGCTGCCAGGTTATGGGTAGCCACTGCCAGGCGGCACCGGGTTCCATCTGGGCCAGCTTCATGACATAACGCGGTTGTTGAGATAAAGCGTCCAGCTTCGGCATTAATAAAGTTTGTGCGGCGTTATAAAAAACCGGTTCGAGATTCTTCGGCAGACTGGTCAACGTTTCGTTACGCAGCAGTTTCGCTA > NC_000913/2334890‑2335152
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
