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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,429,583 |
C→T |
51.5% |
intergenic (‑1/+11) |
wzzE ← / ← rfe |
Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,429,583 | 0 | C | T | 51.5%
| ‑6.4
/ 101.7
| 68 | intergenic (‑1/+11) | wzzE/rfe | Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein/UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase |
| Reads supporting (aligned to +/- strand): ref base C (22/11); new base T (18/17); total (40/28) |
| Fisher's exact test for biased strand distribution p-value = 2.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.87e-01 |
GAAACAACCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGTTT > minE/2429513‑2429644
|
gAAACAACCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGtcatc < 1:1217625/71‑1 (MQ=255)
gAAACAACCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGtcatc < 1:3357615/71‑1 (MQ=255)
acaacCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATcaca < 1:2497980/71‑1 (MQ=255)
acaacCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGGCATcaca < 1:3083184/71‑1 (MQ=255)
ccACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCt > 1:2857595/1‑70 (MQ=255)
aCGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATc < 1:897479/66‑1 (MQ=255)
cGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCatt < 1:2605021/71‑1 (MQ=255)
gAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCatt > 1:866975/1‑70 (MQ=255)
gAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCattt < 1:1968126/71‑1 (MQ=255)
aaTATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCattta > 1:2231221/1‑71 (MQ=255)
cAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCatttattt > 1:1630472/1‑68 (MQ=255)
gTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTa < 1:1879905/71‑1 (MQ=255)
ttCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTaa < 1:3027059/71‑1 (MQ=255)
tCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTaaa > 1:1016876/1‑71 (MQ=255)
tCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTaaa > 1:2073768/1‑71 (MQ=255)
cATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAAt > 1:1114122/1‑71 (MQ=255)
cATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCat > 1:3343085/1‑57 (MQ=255)
cATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAAt > 1:307901/1‑71 (MQ=255)
aTTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAAtt < 1:2047133/71‑1 (MQ=255)
aTTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAAtt < 1:1181469/71‑1 (MQ=255)
ttttCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTg < 1:340166/71‑1 (MQ=255)
ttCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTaaa > 1:2403389/1‑66 (MQ=255)
ttCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTggg > 1:1985225/1‑71 (MQ=255)
tCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCattta < 1:1283545/55‑1 (MQ=255)
tCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCattta < 1:3475749/55‑1 (MQ=255)
aGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTaaa > 1:1596698/1‑63 (MQ=255)
aGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCt < 1:3612998/71‑1 (MQ=255)
gCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTg > 1:2820533/1‑71 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAAtt > 1:3603648/1‑59 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGccac > 1:1474593/1‑70 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGt > 1:1260525/1‑53 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGccac > 1:4076458/1‑70 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGccac > 1:965428/1‑70 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGccac > 1:180527/1‑70 (MQ=255)
ttCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGcca > 1:2829185/1‑69 (MQ=255)
cGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTaaa < 1:3532477/55‑1 (MQ=255)
cGGCCGGTTTCCCAGGCATTGGTTGTGTCATTACATACTCATTTATTTGGTTAAATTGGGGCTGccac < 1:2088678/68‑1 (MQ=255)
cGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCcaccac > 1:3668105/1‑71 (MQ=255)
cGGCCGGTTTCCCACGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAAtt > 1:438139/1‑57 (MQ=255)
ccGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAt < 1:3921932/71‑1 (MQ=255)
ccGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAt < 1:559868/71‑1 (MQ=255)
ccGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAt < 1:3435702/71‑1 (MQ=255)
ccGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAt > 1:3051055/1‑71 (MQ=255)
ccGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAt > 1:357529/1‑71 (MQ=255)
cGGTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGAtt > 1:209223/1‑71 (MQ=255)
gTTTCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGc > 1:2000555/1‑59 (MQ=255)
tttCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCt < 1:3339131/71‑1 (MQ=255)
ttCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTa > 1:2831026/1‑71 (MQ=255)
ttCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTa > 1:740132/1‑71 (MQ=255)
ttCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTa > 1:3580721/1‑71 (MQ=255)
tCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTAc > 1:165212/1‑71 (MQ=255)
tCCCAGGCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTAc > 1:1611373/1‑71 (MQ=255)
cAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAAt < 1:3702372/44‑1 (MQ=255)
cAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTg > 1:1943288/1‑46 (MQ=255)
cAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCa < 1:604324/71‑1 (MQ=255)
aGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTa < 1:1767240/40‑1 (MQ=255)
gCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTc < 1:775066/71‑1 (MQ=255)
gCATTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTc > 1:830488/1‑71 (MQ=255)
aTTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAAt > 1:625075/1‑39 (MQ=255)
aTTGGTTGTGTCATTACATCCTCATTTATTTGGTTAAAt > 1:2390202/1‑39 (MQ=255)
ttGGTTGTGTCATTACATCCTCATTTATTTGGTTaaa < 1:2980626/37‑1 (MQ=255)
ttGGTTGTGTCATTACATCCTCATTTATTTGGTTaaa < 1:2798738/37‑1 (MQ=255)
ttGGTTGTGTCATCACATCCTCATTTATTTGGTTaaa < 1:2456309/37‑1 (MQ=255)
ttGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGc > 1:1163471/1‑71 (MQ=255)
ggTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCg < 1:2005736/70‑1 (MQ=255)
ggTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGt > 1:2761087/1‑71 (MQ=255)
ggTTGTGTCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGt > 1:2667749/1‑71 (MQ=255)
gTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGt < 1:2946284/70‑1 (MQ=255)
tgtgTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCcaccac > 1:1817994/1‑48 (MQ=255)
gtgtCATCACATACTCATTTATTTGGTTAAATTGGGGCTGCCACAACGAt > 1:1216077/1‑50 (MQ=255)
tgtCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGt < 1:3421657/60‑1 (MQ=255)
tgtCATTACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGt < 1:2653066/60‑1 (MQ=255)
tcatcaCATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGttt < 1:1911817/66‑1 (MQ=255)
cacaTCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGtt > 1:2542540/1‑61 (MQ=255)
|
GAAACAACCCACGAATATCCAGTTCATTTTCAGCGTCTTCGGCCGGTTTCCCAGGCATTGGTTGTGTCATCACATCCTCATTTATTTGGTTAAATTGGGGCTGCCACCACGATTTCTACGCAGTCTGCGTTT > minE/2429513‑2429644
|
| 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
