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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 114.0
/ NA
| 34 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (12/22); total (12/22) |
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCA > NZ_CP009273/2345327‑2345494
|
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:97783/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:227796/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 2:492108/90‑1 (MQ=255)
accGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc > 2:168883/1‑67 (MQ=255)
accGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:168883/67‑1 (MQ=255)
accGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcggcgg > 1:535743/1‑90 (MQ=255)
gTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCAccc > 1:641396/1‑90 (MQ=255)
tgtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCa > 1:662147/1‑90 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 1:693867/90‑1 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 2:107874/90‑1 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAATCAACCGCa < 1:111422/90‑1 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 2:629699/90‑1 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 1:669770/90‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:460595/39‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGaacc > 2:49150/1‑82 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGaacc < 1:49150/82‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:696655/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 2:653998/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 2:169286/89‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa > 1:169286/1‑89 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCaga < 2:119149/90‑1 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCaga < 2:48035/90‑1 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCAGCCACCCCATCCCCTGGAACCAACCGCaga < 2:472791/90‑1 (MQ=255)
caATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa < 1:381245/90‑1 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 1:462990/1‑90 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 2:390958/1‑90 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 2:602167/90‑1 (MQ=255)
gccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAg > 2:540902/1‑90 (MQ=255)
gccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAg < 2:541296/90‑1 (MQ=255)
cACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTa < 2:526025/90‑1 (MQ=255)
aCGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAc > 1:118272/1‑90 (MQ=255)
tctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCa < 2:696655/90‑1 (MQ=255)
cGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGc < 1:444222/90‑1 (MQ=255)
gACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCa < 1:137731/90‑1 (MQ=255)
|
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCA > NZ_CP009273/2345327‑2345494
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACG > NZ_CP009273/2345315‑2345504
|
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGG > SRR3722112.174730/1‑100 (MQ=60)
gtataagagacaGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722112.170956/88‑1 (MQ=60)
attgacattcgtcggcagcgtcagatgtgtataagagacagGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722112.467112/59‑1 (MQ=60)
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722112.99004/100‑1 (MQ=60)
GAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGG > SRR3722112.543726/1‑100 (MQ=60)
CACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCC > SRR3722112.651370/1‑100 (MQ=60)
CCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCA > SRR3722112.672474/1‑100 (MQ=60)
GTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAAC < SRR3722112.704705/100‑1 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722112.707543/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722112.171365/1‑100 (MQ=60)
TCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAG < SRR3722112.49752/100‑1 (MQ=60)
CACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC > SRR3722112.469554/1‑100 (MQ=60)
TGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAATCAACCGCAGAGGAACAAC < SRR3722112.112811/100‑1 (MQ=60)
TGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAAC < SRR3722112.680223/100‑1 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC < SRR3722112.386198/100‑1 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC > SRR3722112.119743/1‑100 (MQ=60)
CGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGAC < SRR3722112.450384/100‑1 (MQ=60)
GACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACG < SRR3722112.139446/100‑1 (MQ=60)
|
ATCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACG > NZ_CP009273/2345315‑2345504
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
