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 |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,242,636 |
+A |
intergenic (‑1/+279) |
ygfF ← / ← gcvP |
SDR family oxidoreductase/aminomethyl‑transferring glycine dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,242,635 | 1 | . | A | 100.0%
| 89.0
/ NA
| 25 | M1M (GTG→TTG) † | ygfF | SDR family oxidoreductase |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base A (12/13); total (12/13) |
GCCAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCAC‑AGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGA > NC_017635/3242586‑3242679
|
gcCAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTcac < 2:244168/50‑1 (MQ=255)
ccAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTcac‑a < 2:1259571/50‑1 (MQ=255)
aaCAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTcac‑aag < 1:1845465/50‑3 (MQ=255)
gTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCt < 1:2053932/50‑1 (MQ=255)
gTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCt < 2:1687352/50‑1 (MQ=255)
tAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCta < 1:533849/50‑1 (MQ=255)
tAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCta < 2:1460778/50‑1 (MQ=255)
aTGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCtata < 1:1172960/50‑1 (MQ=255)
aTGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCtata < 1:1711023/50‑1 (MQ=255)
tGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATAg < 2:582518/50‑1 (MQ=255)
ttGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCAtt < 2:315352/50‑1 (MQ=255)
cccgcccgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCACTTg < 2:272703/49‑1 (MQ=38)
gcccgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGtttt > 1:241048/1‑50 (MQ=255)
gcccgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGtttt > 2:1169087/1‑50 (MQ=255)
gcccgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGtttt > 1:1003870/1‑50 (MQ=255)
cgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTcc < 2:1326262/50‑1 (MQ=255)
cgATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTcc > 2:1209264/1‑50 (MQ=255)
gATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCg < 2:841953/50‑1 (MQ=255)
tGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTcc > 2:933141/1‑47 (MQ=255)
gcgACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGaaa > 1:1587897/1‑49 (MQ=255)
gCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAaattaat > 2:991005/1‑50 (MQ=255)
ccACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAaattaat < 1:1750334/49‑1 (MQ=255)
cACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTc < 2:651883/50‑1 (MQ=255)
ccGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGt > 1:525899/1‑50 (MQ=255)
ggTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGtt > 2:1552325/1‑49 (MQ=255)
ggTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGtt > 1:476944/1‑49 (MQ=255)
ggTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGtt > 2:467451/1‑49 (MQ=255)
gTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGa > 2:1542880/1‑50 (MQ=255)
|
GCCAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCAC‑AGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGA > NC_017635/3242586‑3242679
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCAC‑AGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGACGT > NC_017635/3242588‑3242682
|
CAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCAC‑Aag < M01420:85:000000000‑AC936:1:2111:21946:25873/51‑3 (MQ=60)
AGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCT > M01420:85:000000000‑AC936:1:1104:13610:14865/1‑51 (MQ=60)
AGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCT < M01420:85:000000000‑AC936:1:2114:9782:18211/51‑1 (MQ=60)
GTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTA < M01420:85:000000000‑AC936:1:1108:15959:8477/51‑1 (MQ=60)
AATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATA < M01420:85:000000000‑AC936:1:2102:9582:25136/51‑1 (MQ=60)
AATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATA < M01420:85:000000000‑AC936:1:2110:17327:7284/51‑1 (MQ=60)
GCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTT > M01420:85:000000000‑AC936:1:1104:13267:9595/1‑51 (MQ=60)
GCCCGATGCCGCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTT > M01420:85:000000000‑AC936:1:1114:21585:17449/1‑51 (MQ=60)
GCGACTGCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAA > M01420:85:000000000‑AC936:1:2108:27591:15376/1‑50 (MQ=60)
GCCACCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAAT < M01420:85:000000000‑AC936:1:2110:17759:19099/50‑1 (MQ=60)
CCGGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTT > M01420:85:000000000‑AC936:1:1108:13107:5475/1‑51 (MQ=60)
GGTCACAAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTG > M01420:85:000000000‑AC936:1:1107:22537:13605/1‑50 (MQ=60)
acaAGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGACGT > M01420:85:000000000‑AC936:1:2102:8397:7140/4‑50 (MQ=60)
|
CAACAGTAATGCAGTTGCCCGCCCGATGCCGCGACTGCCACCGGTCAC‑AGTGCTATAGCCATTTGTTTTTCCGAGAAAAATTAATTCGTTGACGT > NC_017635/3242588‑3242682
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
