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 |
|
A1 F2 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,318,468 |
A→C |
A609A (GCT→GCG) |
ftsH ← |
ATP‑dependent zinc metalloprotease FtsH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,318,468 | 0 | A | C | 100.0%
| 172.9
/ NA
| 51 | A609A (GCT→GCG) | ftsH | ATP‑dependent zinc metalloprotease FtsH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (22/29); total (22/29) |
ATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCAT > NZ_CP009273/3318385‑3318553
|
aTGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCt < 2:48708/90‑1 (MQ=255)
aTGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCt < 1:332640/90‑1 (MQ=255)
ggTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTgg > 1:214005/1‑90 (MQ=255)
tgtTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGtt < 2:273839/90‑1 (MQ=255)
gtTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGttc < 1:1209438/90‑1 (MQ=255)
gtTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGttc < 1:847524/90‑1 (MQ=255)
tACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGttctt > 1:274761/1‑90 (MQ=255)
gggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAg > 1:331238/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:982300/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:972091/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 1:1050836/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:605552/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGc > 2:1130686/1‑90 (MQ=255)
ggTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGCCGCCAGAATAGTTAGACGCGCCTGGATCTTCCCAGc > 1:550601/1‑90 (MQ=255)
gTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGcc < 1:313507/90‑1 (MQ=255)
cGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGc > 1:79294/1‑90 (MQ=255)
ggCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCt > 1:508353/1‑90 (MQ=255)
gCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTg > 1:589562/1‑90 (MQ=255)
gTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGc < 1:798210/90‑1 (MQ=255)
gTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGc < 2:779683/90‑1 (MQ=255)
gTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGc < 2:915510/90‑1 (MQ=255)
gTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGc < 1:518540/90‑1 (MQ=255)
cgcgGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGa < 1:396464/90‑1 (MQ=255)
ggTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGt < 1:189612/90‑1 (MQ=255)
tcaACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATcg > 1:779216/1‑90 (MQ=255)
tcaACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATcg > 2:29145/1‑90 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg < 2:1050836/90‑1 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg < 2:1077649/90‑1 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg < 2:308949/90‑1 (MQ=255)
cGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATCGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACg > 1:198609/1‑90 (MQ=255)
ggACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGt < 1:588591/90‑1 (MQ=255)
aggagCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCAt > 2:738802/1‑90 (MQ=255)
agCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAg < 2:66537/90‑1 (MQ=255)
ttGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGtcat < 2:938782/90‑1 (MQ=255)
ttGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGtcat < 1:436933/90‑1 (MQ=255)
cTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATc < 1:825609/90‑1 (MQ=255)
taacATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCt > 1:1062716/4‑90 (MQ=255)
tACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCa > 2:57641/1‑75 (MQ=255)
tACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCa < 1:57641/75‑1 (MQ=255)
tACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCt > 1:128998/1‑90 (MQ=255)
ccATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGc < 2:504699/90‑1 (MQ=255)
cATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCg < 1:339809/90‑1 (MQ=255)
gTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGc > 1:1210725/1‑90 (MQ=255)
cGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGtc < 2:126434/73‑1 (MQ=255)
cGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGtc > 1:126434/1‑73 (MQ=255)
aGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGAt < 2:769239/90‑1 (MQ=255)
aGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGAt < 1:463156/90‑1 (MQ=255)
gAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATa > 2:184204/1‑90 (MQ=255)
tAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCat < 2:169019/90‑1 (MQ=255)
tAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCat < 2:79294/90‑1 (MQ=255)
tAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCat < 2:867737/90‑1 (MQ=255)
|
ATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCAT > NZ_CP009273/3318385‑3318553
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATAT > NZ_CP009273/3318372‑3318555
|
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCG < SRR3722089.209506/100‑1 (MQ=60)
GCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGG > SRR3722089.216706/1‑100 (MQ=60)
GACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTT > SRR3722089.278263/1‑100 (MQ=60)
atctacactaagatggtcgtcggcagcgtcagatgtgtataagagacAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCC < SRR3722089.1061210/53‑1 (MQ=60)
ATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCC < SRR3722089.336799/100‑1 (MQ=60)
GGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAG > SRR3722089.335381/1‑100 (MQ=60)
GTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGC > SRR3722089.1066588/1‑100 (MQ=60)
GTGTAACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGCCGCCAGAATAGTTAGACGCGCCTGGATCTTCCCAGC > SRR3722089.556995/1‑100 (MQ=60)
GTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCC < SRR3722089.859577/100‑1 (MQ=60)
GTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCC < SRR3722089.1227823/100‑1 (MQ=60)
TACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGC > SRR3722089.80264/1‑100 (MQ=60)
ACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCT > SRR3722089.514340/1‑100 (MQ=60)
acaGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTG > SRR3722089.596697/4‑100 (MQ=60)
GTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGA < SRR3722089.317482/100‑1 (MQ=60)
GTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACAT < SRR3722089.809233/100‑1 (MQ=60)
GTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACAT < SRR3722089.524625/100‑1 (MQ=60)
ACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCG > SRR3722089.789819/1‑100 (MQ=60)
CGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGC < SRR3722089.401290/100‑1 (MQ=60)
GGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGAC < SRR3722089.191987/100‑1 (MQ=60)
GTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATCGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACG > SRR3722089.201118/1‑100 (MQ=60)
GGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGT < SRR3722089.595705/100‑1 (MQ=60)
gacagGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATC < SRR3722089.58349/95‑1 (MQ=60)
GCCTTTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCT > SRR3722089.130565/1‑100 (MQ=60)
GCCTTTGGACTAACATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCT > SRR3722089.1078672/1‑100 (MQ=60)
TTGGACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGG < SRR3722089.442187/100‑1 (MQ=60)
GACTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGC > SRR3722089.1229137/1‑100 (MQ=60)
CTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCctgtctc > SRR3722089.127977/1‑93 (MQ=60)
CTACCATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGT < SRR3722089.837251/100‑1 (MQ=60)
CATTGTCGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGAT < SRR3722089.344039/100‑1 (MQ=60)
CGCCAGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCtgtctcttatacacatctgacgctgccgacgaccatcttagtgta > SRR3722089.18789/1‑55 (MQ=60)
AGAATTGTTAGACGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATAT < SRR3722089.468684/100‑1 (MQ=60)
|
TAACTGCTCTGACATGGTGTTACCCGGGTTCGGCGTACGCGGTTCATCAACCGGACGAGGAGCCTTTGGACTACCATTGTCGCCAGAATTGTTAGAAGCGCCTGGTTCTTCCCAGCCCGCTGGCGGACGTACATCGCGACGTGCCATCAGGTCATCAATCTGCGGTGCGTCGATAGTCTCATAT > NZ_CP009273/3318372‑3318555
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
