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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,345,414 |
T→G |
H147P (CAC→CCC) |
glpT ← |
glycerol‑3‑phosphate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,345,414 | 0 | T | G | 100.0%
| 103.0
/ NA
| 29 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (13/16); total (13/16) |
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATC > NZ_CP009273/2345327‑2345488
|
aaCAGCAGCGGCGGAATACCCCCCCCGACGTTGTGCGCCCAGTTCCACCCTGACCCAATGCCCCCACGTTCTTTCTGCGACCACCAGGGc < 2:300346/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGCCGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:37408/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:154609/90‑1 (MQ=255)
aCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCa < 1:84690/90‑1 (MQ=255)
agcagcGGCGGAATACCACCCCCGACGTTGTGCGCACAGTTCCACACGGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 2:495542/90‑1 (MQ=255)
ggcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTa > 1:177504/1‑90 (MQ=255)
gcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAc < 2:813272/90‑1 (MQ=255)
caccGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcggcg > 1:318537/1‑90 (MQ=255)
caccGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcggcg > 1:556852/1‑90 (MQ=255)
accGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc > 2:45359/1‑67 (MQ=255)
accGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:45359/67‑1 (MQ=255)
gtgCGCACAGTTCCACCCTGACACAATGCCGCCACGTTCTTTCTGCAACCACCAGGGCACCATAGTTCGCCCACACGGCGGCCACCCCAt < 2:901918/90‑1 (MQ=255)
caGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCCCCATAGTACGACCACACGGCGGCCACCCCATCCCCTgg < 1:838811/90‑1 (MQ=255)
gTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGaa > 1:126581/1‑90 (MQ=255)
cTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:665376/41‑1 (MQ=255)
cTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGc > 2:748756/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATcccc < 2:221306/75‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATcccc > 1:221306/1‑75 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 2:563512/1‑90 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCaga < 2:177504/90‑1 (MQ=255)
caATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa < 1:660858/90‑1 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 2:706034/1‑90 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 1:162166/1‑90 (MQ=255)
ccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGt > 1:109180/1‑90 (MQ=255)
aCGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa < 1:190943/80‑1 (MQ=255)
aCGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa > 2:190943/1‑80 (MQ=255)
ttctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATc < 1:386283/90‑1 (MQ=255)
ctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 1:219822/48‑1 (MQ=255)
ctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt > 2:219822/1‑48 (MQ=255)
|
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATC > NZ_CP009273/2345327‑2345488
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 29 ≤ 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
GAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGC > NZ_CP009273/2345326‑2345498
|
GAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTA > SRR3722072.180579/1‑100 (MQ=60)
gtataagagacaGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722072.46187/88‑1 (MQ=60)
ACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACG < SRR3722072.86271/100‑1 (MQ=60)
GGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCG > SRR3722072.324115/1‑100 (MQ=60)
GGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCG > SRR3722072.566860/1‑100 (MQ=60)
TGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAA > SRR3722072.128877/1‑100 (MQ=60)
ctcgtgggctcggagatgtgtataagagacagCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAAC < SRR3722072.223559/68‑1 (MQ=60)
CAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCCCCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGC < SRR3722072.853347/100‑1 (MQ=60)
CAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACctgtctcttatacacatctccgagcccacgagacgtccg > SRR3722072.677274/1‑61 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCtgtc > SRR3722072.225064/1‑96 (MQ=60)
CACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC > SRR3722072.164991/1‑100 (MQ=60)
CACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGT > SRR3722072.111199/1‑100 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC < SRR3722072.194254/100‑1 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC < SRR3722072.672655/100‑1 (MQ=60)
TTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGC < SRR3722072.393193/100‑1 (MQ=60)
|
GAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGC > NZ_CP009273/2345326‑2345498
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
