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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,057,873 |
C→G |
W418C (TGG→TGC) |
yihO ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,057,873 | 0 | C | G | 100.0%
| 91.6
/ NA
| 27 | W418C (TGG→TGC) | yihO | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (17/10); total (17/10) |
AATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATA > NZ_CP009273/4057799‑4057957
|
aaTGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGc < 2:263496/90‑1 (MQ=255)
aaCCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGc > 2:29400/1‑90 (MQ=255)
ccGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCaa < 2:202998/90‑1 (MQ=255)
ccGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCaa < 1:139738/90‑1 (MQ=255)
gAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGt > 2:442361/1‑90 (MQ=255)
gtgtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCa > 2:301067/1‑90 (MQ=255)
gAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTg > 1:350217/1‑90 (MQ=255)
gAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTg > 1:60005/1‑90 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 1:436588/1‑90 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 2:153919/1‑90 (MQ=255)
aTCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg < 1:285495/85‑1 (MQ=255)
aTCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 2:285495/1‑85 (MQ=255)
aaTGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGa < 1:17832/90‑1 (MQ=255)
aTGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGaa > 2:33232/1‑90 (MQ=255)
aTGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGaa > 2:340718/1‑90 (MQ=255)
gcagcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACa < 1:183982/90‑1 (MQ=255)
gcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATaa > 2:82885/1‑90 (MQ=255)
gcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATaa > 1:222896/1‑90 (MQ=255)
aatTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAAt > 2:399109/1‑90 (MQ=255)
aatTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAAt > 1:193120/1‑90 (MQ=255)
gCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGc < 2:436588/90‑1 (MQ=255)
ccAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCg > 2:16764/1‑90 (MQ=255)
aGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTc < 1:301067/90‑1 (MQ=255)
gTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTc > 2:208830/1‑89 (MQ=255)
gTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTc < 1:208830/89‑1 (MQ=255)
gCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGc > 2:390343/1‑90 (MQ=255)
caAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATa < 1:302884/90‑1 (MQ=255)
|
AATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATA > NZ_CP009273/4057799‑4057957
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCA > NZ_CP009273/4057807‑4057967
|
CCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAAT < SRR3722087.141033/100‑1 (MQ=60)
GTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTG > SRR3722087.354141/1‑100 (MQ=60)
GTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTG > SRR3722087.60520/1‑100 (MQ=60)
GTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCG > SRR3722087.441690/1‑100 (MQ=60)
ATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGG < SRR3722087.288367/100‑1 (MQ=60)
CGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAA > SRR3722087.224898/1‑100 (MQ=60)
AATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAA < SRR3722087.17970/100‑1 (MQ=60)
ATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAAT > SRR3722087.194818/1‑100 (MQ=60)
GCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTT < SRR3722087.185614/100‑1 (MQ=60)
AGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGC < SRR3722087.210656/100‑1 (MQ=60)
AGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGC < SRR3722087.304187/100‑1 (MQ=60)
GTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGActgtctcttatacacatctccgagcccac > SRR3722087.296998/1‑71 (MQ=60)
CAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCA < SRR3722087.306030/100‑1 (MQ=60)
|
CCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTGGCA > NZ_CP009273/4057807‑4057967
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
