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 |
|
A5 F17 I0 R2
|
162 |
60.6 |
4616657 |
98.5% |
4547407 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,735,429 |
G→A |
13.0% |
A323T (GCA→ACA) |
bglH → |
carbohydrate‑specific outer membrane porin, cryptic |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,735,429 | 0 | G | A | 13.0%
| 194.7
/ 16.4
| 69 | A323T (GCA→ACA) | bglH | carbohydrate‑specific outer membrane porin, cryptic |
| Reads supporting (aligned to +/- strand): ref base G (40/20); new base A (3/6); total (43/26) |
| Fisher's exact test for biased strand distribution p-value = 7.18e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
AGATATCCCGTTATGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGCACAT > W3110S.gb/3735362‑3735498
|
aGATATCCCGTTATGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCa > 1:1241909/1‑70 (MQ=255)
aGATATCCCGTTATGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCAt > 1:1577846/1‑71 (MQ=255)
cccGTTATGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGaa > 1:110677/1‑70 (MQ=255)
tGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATa < 1:437396/70‑1 (MQ=255)
ggATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCACATCg < 1:4240830/58‑1 (MQ=255)
ggATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCACATCGGAAAAAGATAAt < 1:1986990/70‑1 (MQ=255)
gATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCa < 1:3236721/71‑1 (MQ=255)
gATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCACATCGGAAAAAGATAAt > 1:3647970/1‑69 (MQ=255)
aaaGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGa > 1:613475/1‑71 (MQ=255)
aaaGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGa > 1:762663/1‑71 (MQ=255)
aGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATc > 1:3775903/1‑65 (MQ=255)
gCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGataa > 1:63451/1‑71 (MQ=255)
ccACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGataat < 1:3723255/71‑1 (MQ=255)
cACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGat > 1:2770049/1‑67 (MQ=255)
cACCTTAATGGTAAGTGGTCGTTATGGCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGat > 1:3943907/1‑67 (MQ=255)
ccTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAAc > 1:3061599/1‑71 (MQ=255)
cTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGAtaataa > 1:4058196/1‑69 (MQ=255)
aaTGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg < 1:4154125/70‑1 (MQ=255)
gTAAGTGGTCGTTATGTCACGGCAAACGAAAGCACATCGGAAAAAGATAATCAGGATAATAACGGGtatta < 1:1524966/71‑1 (MQ=255)
tAAGTGGTCGTTATGTCCCGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGtatt < 1:3759706/69‑1 (MQ=255)
tAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGtattat < 1:3754481/71‑1 (MQ=255)
gTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg > 1:949483/1‑62 (MQ=255)
gTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGTGTATTATGAc < 1:1086422/71‑1 (MQ=255)
gTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGt > 1:1070740/1‑63 (MQ=255)
gTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGAc < 1:3307508/71‑1 (MQ=255)
tGGTCGATATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATaa > 1:4575297/1‑45 (MQ=255)
gttCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGata > 1:2534799/3‑52 (MQ=255)
ggTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATaa > 1:1168889/1‑44 (MQ=255)
gTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTg < 1:2720148/70‑1 (MQ=255)
gTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTg < 1:1310850/70‑1 (MQ=255)
tCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg < 1:397965/58‑1 (MQ=255)
tCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa < 1:311577/71‑1 (MQ=255)
tCGTTATGTCACGGCAAACGAAAGCACATCGGAAAAAGATAATCAGGATAATAACGGGTATTATg < 1:1603127/65‑1 (MQ=255)
cGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAgg > 1:4347890/1‑46 (MQ=255)
cGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa > 1:838588/1‑70 (MQ=255)
gTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCATGATAATAACGGGTATTATGACTGGaaa < 1:832800/71‑1 (MQ=255)
gTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg < 1:118057/56‑1 (MQ=255)
gTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa > 1:4252503/1‑69 (MQ=255)
gTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa > 1:3252735/1‑69 (MQ=255)
ttttGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGtattat < 1:3295593/58‑1 (MQ=255)
tATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGaaa > 1:2186976/1‑69 (MQ=255)
tATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa > 1:3379548/1‑67 (MQ=255)
aTGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGataat > 1:2465450/1‑47 (MQ=255)
gTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg < 1:2282640/51‑1 (MQ=255)
gTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATAc > 1:694248/1‑71 (MQ=255)
cACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAgg > 1:2944018/1‑38 (MQ=255)
aCGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAAc > 1:1726383/1‑45 (MQ=255)
aCGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAAc > 1:2986769/1‑45 (MQ=255)
aCGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTg > 1:4567935/1‑71 (MQ=255)
aCGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTg < 1:430687/71‑1 (MQ=255)
aCGGCAAACGAAAGCACATCGGAAAAAGATAATCAGGATAATAGCGGGTATTATGACt < 1:3965932/58‑1 (MQ=255)
cGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGtatta > 1:1931776/1‑52 (MQ=255)
cGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTg > 1:3570816/1‑70 (MQ=255)
cGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTg > 1:651367/1‑70 (MQ=255)
cAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTgg > 1:2771534/1‑56 (MQ=255)
cAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATg > 1:3605967/1‑71 (MQ=255)
aaaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGt > 1:981888/1‑71 (MQ=255)
aaaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGt < 1:4520330/71‑1 (MQ=255)
aaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACggg < 1:4158729/42‑1 (MQ=255)
aaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGt > 1:572110/1‑43 (MQ=255)
aaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGt > 1:2159920/1‑43 (MQ=255)
aaCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAg > 1:2002108/1‑58 (MQ=255)
aCGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGttt > 1:2567570/1‑71 (MQ=255)
aCGAAAGCACATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACt > 1:2828654/1‑51 (MQ=255)
aCGAAAGCACATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGttt < 1:94274/71‑1 (MQ=255)
cGAAAGCACATCGGAAAAAGATAATCAGGAtaataa > 1:3307212/1‑36 (MQ=255)
gAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGa < 1:564757/52‑1 (MQ=255)
aaGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGca > 1:685449/1‑71 (MQ=255)
aGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGca > 1:2284043/1‑70 (MQ=255)
gcgcATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGcaca < 1:2172731/71‑1 (MQ=255)
cgcATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGc > 1:4276291/1‑67 (MQ=255)
gcATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGCACAt < 1:2285607/70‑1 (MQ=255)
|
AGATATCCCGTTATGGGATAAAGCCACCTTAATGGTAAGTGGTCGTTATGTCACGGCAAACGAAAGCGCATCGGAAAAAGATAATCAGGATAATAACGGGTATTATGACTGGAAAGATACCTGGATGTTTGGCACAT > W3110S.gb/3735362‑3735498
|
| 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
