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 I221 R1
|
7 |
18.7 |
1143996 |
96.4% |
1102812 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,269,479 |
T→C |
V243A (GTC→GCC) |
yejE → |
ABC transporter permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,269,479 | 0 | T | C | 100.0%
| 81.9
/ NA
| 25 | V243A (GTC→GCC) | yejE | ABC transporter permease |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/12); total (13/12) |
AGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGTCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTA > NZ_CP009273/2269400‑2269562
|
aGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGc < 2:419930/90‑1 (MQ=255)
aGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGc < 2:394722/90‑1 (MQ=255)
aGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGc < 2:469323/90‑1 (MQ=255)
tGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTa < 2:83644/90‑1 (MQ=255)
ggTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTat > 1:52492/1‑90 (MQ=255)
gtggtgCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTg < 1:150607/90‑1 (MQ=255)
ggcggAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCatat > 1:469322/1‑90 (MQ=255)
cggAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGt < 2:469322/90‑1 (MQ=255)
gAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTg > 1:49216/1‑90 (MQ=255)
gTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGcc > 2:459969/1‑90 (MQ=255)
ttttACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTa < 2:52492/90‑1 (MQ=255)
ttACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAAt > 2:411572/1‑90 (MQ=255)
gTACTCGTAATTTCGAGTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCa > 2:431708/1‑90 (MQ=255)
gTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCa > 2:479140/1‑90 (MQ=255)
ttcTCGTACTTTCGACTACATTCGTGCGGCACCGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCAt < 2:294965/88‑1 (MQ=255)
tACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCAt < 2:49216/90‑1 (MQ=255)
aCTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATg > 2:364557/1‑90 (MQ=255)
gACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTc < 2:248567/90‑1 (MQ=255)
tGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTAcc > 2:524546/1‑90 (MQ=255)
gcTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATg > 1:375783/1‑90 (MQ=255)
cTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGt < 1:364557/90‑1 (MQ=255)
ttGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGt < 1:223028/39‑1 (MQ=39)
ttGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGt > 2:223028/1‑39 (MQ=39)
ttGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTa > 2:270957/1‑90 (MQ=255)
ttGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTa > 2:92850/1‑90 (MQ=255)
|
AGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGTCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTA > NZ_CP009273/2269400‑2269562
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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
GGATGAGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGTCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTAGTTCGATAA > NZ_CP009273/2269395‑2269571
|
GGATGAGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTAT > SRR3722105.53059/1‑100 (MQ=60)
GCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATAT > SRR3722105.475564/1‑100 (MQ=60)
GTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGT < SRR3722105.152241/100‑1 (MQ=60)
GGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTG > SRR3722105.49758/1‑100 (MQ=60)
ggggtacgtctcgtgggctcggagatgtgtataagagacaGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGC < SRR3722105.225385/60‑1 (MQ=60)
CGGCACAGGCGCTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATG > SRR3722105.380509/1‑100 (MQ=60)
CTTGGCGCCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTAGTTCGATAA < SRR3722105.369078/100‑1 (MQ=60)
|
GGATGAGTCTGGTCGGCGTGGTGCGGGCGGAGTTTTTACGTACTCGTAATTTCGACTACATTCGTGCGGCACAGGCGCTTGGCGTCAGCGATCGCAGTATCATCCTGCGTCATATGTTGCCTAATGCCATGGTCGCGACCCTCACCTTTTTACCGTTTATTTTATGTAGTTCGATAA > NZ_CP009273/2269395‑2269571
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
