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 I208 R1
|
222 |
13.1 |
731276 |
96.6% |
706412 |
85.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,505,986 |
T→C |
intergenic (‑283/+7) |
BW25113_RS17530 ← / ← trpS |
GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,505,986 | 0 | T | C | 100.0%
| 66.2
/ NA
| 19 | intergenic (‑283/+7) | BW25113_RS17530/trpS | GntR family transcriptional regulator YhfZ/tryptophan‑‑tRNA ligase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/7); total (12/7) |
TCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGC > NZ_CP009273/3505902‑3506061
|
tCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGa > 1:332788/1‑90 (MQ=255)
tgtgCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTc < 1:314972/90‑1 (MQ=255)
ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAAcc > 1:89221/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 1:287921/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 2:201488/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 2:118583/1‑90 (MQ=255)
ccGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCt > 1:71353/1‑90 (MQ=255)
ggATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTc > 1:268179/1‑90 (MQ=255)
aGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTaca < 2:133570/90‑1 (MQ=255)
ttCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCcac < 2:76064/65‑1 (MQ=255)
ttCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGGGAATTACGGCTTCGCcac > 1:76064/1‑65 (MQ=255)
tCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt > 1:54027/1‑90 (MQ=255)
tCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCtt > 1:271215/1‑90 (MQ=255)
ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc > 1:289872/1‑90 (MQ=255)
ccgcATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGc < 2:287921/90‑1 (MQ=255)
aTCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTAc < 2:272187/90‑1 (MQ=255)
aGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTgcgcgc < 2:268179/90‑1 (MQ=255)
aGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTgcgcgc < 2:271215/90‑1 (MQ=255)
cAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGc > 1:299683/1‑90 (MQ=255)
|
TCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGC > NZ_CP009273/3505902‑3506061
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ 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
GGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCAT > NZ_CP009273/3505892‑3506082
|
GGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGA < SRR3722090.185368/100‑1 (MQ=60)
GGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGA > SRR3722090.337124/1‑100 (MQ=60)
TGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAAC < SRR3722090.319045/100‑1 (MQ=60)
GTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACC > SRR3722090.90195/1‑100 (MQ=60)
ACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCT > SRR3722090.291526/1‑100 (MQ=60)
ACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCT > SRR3722090.72137/1‑100 (MQ=60)
TTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTC > SRR3722090.271483/1‑100 (MQ=60)
GGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGGGAATTACGGCTTCGCCACAAAACCAATCctgtctcttatacac > SRR3722090.76903/1‑85 (MQ=60)
GATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTT > SRR3722090.274566/1‑100 (MQ=60)
GATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTT > SRR3722090.54608/1‑100 (MQ=60)
GGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGC > SRR3722090.293502/1‑100 (MQ=60)
GAACAAAGCGCAATTTGCCAGCAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGC > SRR3722090.303485/1‑100 (MQ=60)
CAACAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCAT > SRR3722090.194273/1‑100 (MQ=60)
|
GGCCTACATTTCCTTGCAATATGTGCATTACTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAAAGCGCAATTTGCCAGCAATAGTGAATTACGGCTTCGCCACAAAACCAATCGCTTCGTACACCGCTTTTAGCGTACGGGAAGCGTGCGCGCTGGCTTTTTCCGCGCCATCTTTCAT > NZ_CP009273/3505892‑3506082
|
| 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: ‑ |
