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 |
261,102 |
C→T |
33.2% |
P73P (CCG→CCA) |
yajI ← |
predicted lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 261,102 | 0 | C | T | 33.2%
| 50.2
/ 31.0
| 63 | P73P (CCG→CCA) | yajI | predicted lipoprotein |
| Reads supporting (aligned to +/- strand): ref base C (31/11); new base T (6/15); total (37/26) |
| Fisher's exact test for biased strand distribution p-value = 9.65e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.62e-01 |
CCATCTGCATCAGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGC > minE/261034‑261156
|
ccATCTGCATCAGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGcc > 1:852128/1‑69 (MQ=255)
tGCATCAGGCGTAATATTCACCAGCGACATACGTAAATTACCGATCTGGCTTTCCAGTCTTGCCGgtgt > 1:2742813/1‑69 (MQ=255)
tGCATCAGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGgtgt > 1:2673310/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGTTTTTGc > 1:15710/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGTTTTTGc > 1:1940665/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGTTTTTGc > 1:152231/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGTTTTTGc > 1:399644/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGTTTTTGc > 1:523321/1‑69 (MQ=255)
aGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTATCCAGTCTTGCTGGTGTTTTTGc > 1:3379486/1‑69 (MQ=255)
atatTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTc > 1:2354718/1‑60 (MQ=255)
atatTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCa > 1:347939/1‑66 (MQ=255)
atatTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCa > 1:74392/1‑66 (MQ=255)
atatTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCa > 1:997930/1‑66 (MQ=255)
ttCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGa > 1:1541961/1‑69 (MQ=255)
ttCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGa > 1:2154569/1‑69 (MQ=255)
cAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa < 1:2832718/69‑1 (MQ=255)
cAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa < 1:1746527/69‑1 (MQ=255)
cGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAc < 1:3229922/69‑1 (MQ=255)
cATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc < 1:1232966/69‑1 (MQ=255)
cATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc < 1:187004/69‑1 (MQ=255)
cGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc > 1:539520/1‑65 (MQ=255)
cGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc > 1:1382605/1‑65 (MQ=255)
cGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc > 1:2393135/1‑65 (MQ=255)
cGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAAcccc > 1:2794669/1‑65 (MQ=255)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2017719/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:763606/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:40480/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:1433129/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:3085049/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2980926/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2941386/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2883900/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:1595177/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:1602836/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:161744/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2490795/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2406054/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:2139525/42‑3 (MQ=38)
gTAAAGTACCGATCTGGCTTTCCAGTCTTGCTGGTGtttttg < 1:226423/42‑3 (MQ=38)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:576485/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:2035505/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:491026/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:1275639/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:86279/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTa > 1:2304652/1‑55 (MQ=255)
aaGTACCGATCTGGCTTTCCACTCTTGCCGGTGTTTTCGCTCCAGGCAGAAg > 1:2470358/1‑52 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:1592062/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:979630/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:1275057/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:1972407/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:150985/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:447110/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:2089607/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAttt > 1:1087553/1‑68 (MQ=255)
ccGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGAtt > 1:996878/1‑67 (MQ=255)
cTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCa > 1:2750622/1‑67 (MQ=255)
cTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTc > 1:3230968/1‑57 (MQ=255)
cTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTc > 1:2890210/1‑57 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:1888243/57‑1 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:1575087/57‑1 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:3259284/57‑1 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:862038/57‑1 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:2260548/57‑1 (MQ=255)
gCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGc < 1:2785024/57‑1 (MQ=255)
|
CCATCTGCATCAGGCGTAATATTCACCAGCGACATACGTAAAGTACCGATCTGGCTTTCCAGTCTTGCCGGTGTTTTCGCTCCAGGCAGAAGGTAAACCCCACTGCTGGATTTTGCATTCAGC > minE/261034‑261156
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
