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 |
1,837,471 |
G→A |
6.6% |
I316I (ATC→ATT) |
nlpD ← |
predicted outer membrane lipoprotein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,837,471 | 0 | G | A | 6.6%
| 183.0
/ 2.6
| 61 | I316I (ATC→ATT) | nlpD | predicted outer membrane lipoprotein |
| Reads supporting (aligned to +/- strand): ref base G (23/33); new base A (2/2); total (25/36) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.25e-01 |
TCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGC > minE/1837403‑1837539
|
tcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:516744/1‑71 (MQ=255)
tcttGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtgat > 1:843331/1‑71 (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)
tgttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt > 1:2945745/1‑71 (MQ=255)
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:2780036/71‑1 (MQ=255)
ttCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCa < 1:1513270/71‑1 (MQ=255)
ggACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTtg > 1:913843/1‑56 (MQ=255)
ggACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATATTCAGATTa < 1:2477886/71‑1 (MQ=255)
gACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTAc < 1:1708500/71‑1 (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)
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 > 1:670465/1‑70 (MQ=255)
tCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa < 1:2246373/70‑1 (MQ=255)
tATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAAt < 1:3247433/46‑1 (MQ=255)
tATGGGCGTAAGCCGTAATGTAATCTTCACTGTGTTTAATCATGATGAGATTACCGTAGCCACGCAgctgg > 1:288756/1‑68 (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)
tCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATaa < 1:516533/68‑1 (MQ=255)
tCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac > 1:3068424/1‑70 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaac > 1:378996/1‑71 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa < 1:1070597/70‑1 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaaca < 1:75407/69‑1 (MQ=255)
aGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaaca < 1:1767053/69‑1 (MQ=255)
tAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaac < 1:945665/65‑1 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGc < 1:2715970/39‑1 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:1478642/1‑71 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:1665630/1‑71 (MQ=255)
aaTCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg > 1:2244393/1‑71 (MQ=255)
atcatcATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa < 1:3049118/65‑1 (MQ=255)
atcatcATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCgg < 1:3259269/70‑1 (MQ=255)
tcatcaTTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt < 1:2468349/49‑1 (MQ=255)
catcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCa > 1:678726/1‑71 (MQ=255)
atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGt > 1:2459048/1‑47 (MQ=255)
atcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAAcgcg > 1:1814366/1‑66 (MQ=255)
tcatTATGTTTGATGATAATCAGATTACCGTAGCCGCGCa < 1:1202875/40‑1 (MQ=255)
catTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCt > 1:1103903/1‑71 (MQ=255)
atTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCt < 1:1718874/70‑1 (MQ=255)
tATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCg > 1:1840381/1‑71 (MQ=255)
aTGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaa > 1:1266913/1‑56 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAaacaac > 1:3198838/1‑56 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGt < 1:2668504/71‑1 (MQ=255)
tGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGt < 1:2908566/71‑1 (MQ=255)
gTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTc > 1:3164968/1‑71 (MQ=255)
tgatgaTAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTcgc < 1:537095/70‑1 (MQ=255)
|
TCTTGTTGTTCCCGGACCAGCATTGTGTCGTTATGGGCGTAGGCACTCAGGTAATCATCATTATGTTTGATGATAATCAGATTACCGTAGCCGCGCAGCGCGTTACCAGCATAAACAACGCGGCCATCTGCGGTCGC > minE/1837403‑1837539
|
| 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
