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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,837,447 |
A→C |
8.0% |
S324R (AGT→AGG) ‡ |
nlpD ← |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,837,447 | 0 | A | C | 8.0%
| 186.7
/ 10.9
| 75 | S324R (AGT→AGG) ‡ | nlpD | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base A (30/39); new base C (2/4); total (32/43) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01 |
GCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAA > minE/1837379‑1837517
|
gCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACt < 1:3616542/71‑1 (MQ=255)
cTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACt < 1:313895/70‑1 (MQ=255)
tATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACt > 1:2818512/1‑69 (MQ=255)
aaTTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACt > 1:31308/2‑69 (MQ=255)
ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCAc < 1:1961249/66‑1 (MQ=255)
ttttttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAgg > 1:2156250/1‑71 (MQ=255)
tttGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTa < 1:1277497/70‑1 (MQ=255)
cGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat > 1:1727559/1‑71 (MQ=255)
cGCCTTAACTTCTTGTTGTTCACGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat > 1:2750748/1‑71 (MQ=255)
gCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATcatcat > 1:1904699/1‑70 (MQ=255)
ccTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAatcat < 1:1041345/66‑1 (MQ=255)
ccTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAatcat < 1:66774/66‑1 (MQ=255)
tAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCa > 1:3282239/1‑50 (MQ=255)
aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGt < 1:1687057/56‑1 (MQ=255)
aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGt < 1:945152/56‑1 (MQ=255)
aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGtt > 1:522833/1‑71 (MQ=255)
aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt < 1:2879623/70‑1 (MQ=255)
aaCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt < 1:3181459/70‑1 (MQ=255)
aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt > 1:1503223/1‑71 (MQ=255)
aCTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGttt < 1:215606/71‑1 (MQ=255)
tcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:843331/1‑71 (MQ=255)
tcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:516744/1‑71 (MQ=255)
cttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:1585412/1‑70 (MQ=255)
cttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:3154417/1‑70 (MQ=255)
cttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtga < 1:2772467/69‑1 (MQ=255)
cttGTTGTTCCAGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtga > 1:350049/1‑69 (MQ=255)
gttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCa > 1:3332903/1‑45 (MQ=255)
ttgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa > 1:2838518/1‑58 (MQ=255)
tgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt > 1:2945745/1‑71 (MQ=255)
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:1513270/71‑1 (MQ=255)
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:2780036/71‑1 (MQ=255)
tCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGt > 1:3174707/1‑57 (MQ=255)
ggACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtg > 1:913843/1‑56 (MQ=255)
ggACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATATTCAGATTa < 1:2477886/71‑1 (MQ=255)
gACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc < 1:1708500/71‑1 (MQ=255)
ccAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGttta < 1:3076497/53‑2 (MQ=255)
ccAGCATCGTGTCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGttta < 1:1363628/53‑2 (MQ=255)
cAGCATTGTGTCTTTATGGGCGTAGGCACTCAGGTAATCATCATTAt < 1:2330948/47‑1 (MQ=255)
cAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTAt < 1:2039928/47‑1 (MQ=255)
aGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATg < 1:987331/47‑1 (MQ=255)
aGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatg < 1:1079287/54‑1 (MQ=255)
aGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTa < 1:2449955/71‑1 (MQ=255)
gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgatga < 1:1735045/54‑1 (MQ=255)
gCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAg > 1:3641026/1‑71 (MQ=255)
cATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACAGTAGc > 1:1810632/1‑71 (MQ=255)
atcgtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGcc < 1:287334/68‑1 (MQ=255)
gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa > 1:1212387/1‑39 (MQ=255)
gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTa > 1:2636773/1‑39 (MQ=255)
gtgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATaa > 1:2266130/1‑52 (MQ=255)
gtgtCATTATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTATAATCATGATGAGATTACCGTAGCcacg < 1:83117/71‑1 (MQ=255)
tgtCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc < 1:1774504/60‑1 (MQ=255)
tcattATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAg > 1:2101558/4‑71 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTa < 1:3163641/57‑1 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa < 1:2246373/70‑1 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa > 1:670465/1‑70 (MQ=255)
ttATGGGCGTAGGCACTCAGGTAATCATCATTATGttt < 1:1928413/38‑1 (MQ=255)
tATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt < 1:3247433/46‑1 (MQ=255)
tATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctgg > 1:288756/1‑68 (MQ=255)
aTGGGCGTAGGCACTCAGGTAATCATCATTATGttt > 1:3449705/1‑36 (MQ=255)
aTGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa > 1:3081708/1‑47 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTTATGATAATCAGATTACCg < 1:1727758/54‑1 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGtt < 1:750420/71‑1 (MQ=255)
tGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:3286115/70‑1 (MQ=255)
gggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAcc > 1:2829722/1‑52 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTa < 1:2046195/70‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTa < 1:3128388/70‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc < 1:687821/71‑1 (MQ=255)
ggCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc < 1:833221/71‑1 (MQ=255)
gCGTAGGCACTCAGGTAATCATCATTATGTTtgat < 1:3308793/35‑1 (MQ=255)
gCGTAGGCACTCAGGTAATCATCATTATGTTtgat < 1:1209699/35‑1 (MQ=255)
gCGTAGGCACTCAGGTAATCATCATTATGTTtgat < 1:106110/35‑1 (MQ=255)
gCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc > 1:2730153/1‑70 (MQ=255)
cGTAGGCACTCATGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTAc > 1:1820492/1‑69 (MQ=255)
ggCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGc > 1:2462040/1‑69 (MQ=255)
gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa < 1:1055642/71‑1 (MQ=255)
gCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATa < 1:1534082/71‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGt < 1:1516067/44‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:2787297/59‑1 (MQ=255)
aCTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATaaa < 1:2676144/71‑1 (MQ=255)
|
GCTATTTTTTGCCCCGCCTTAACTTCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAA > minE/1837379‑1837517
|
| 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
