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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 93.1
/ NA
| 27 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (11/16); total (11/16) |
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTC > NZ_CP009273/2345327‑2345500
|
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:301165/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:772066/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 2:89181/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:672372/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:411645/90‑1 (MQ=255)
cggcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGt < 1:156635/90‑1 (MQ=255)
ggcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTa > 1:678898/1‑90 (MQ=255)
accaccGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg < 2:124216/90‑1 (MQ=255)
cGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGcc > 2:543642/1‑90 (MQ=255)
tgtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCa < 2:326107/90‑1 (MQ=255)
gcgcACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATcc > 1:622220/1‑90 (MQ=255)
tGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCa < 1:142202/90‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:305873/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:748749/1‑90 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCaga < 1:768183/90‑1 (MQ=255)
acacAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCaga < 1:602305/90‑1 (MQ=255)
caATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa < 2:193403/90‑1 (MQ=255)
aTGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaac > 1:388140/1‑90 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 1:358484/90‑1 (MQ=255)
gccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAg > 1:465350/1‑90 (MQ=255)
ccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGt > 1:76493/1‑90 (MQ=255)
aCGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAc > 1:212414/1‑90 (MQ=255)
gTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATc < 1:21720/56‑1 (MQ=255)
gTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATc > 2:21720/1‑56 (MQ=255)
ttctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATc < 2:298240/90‑1 (MQ=255)
gACCACCAGGGCACCATAGTACGACCACACGGCGTCCACCCCATCCCCAGGAACCAACGGCGGTGGAACAACAGTACAAGCATCACCTCa > 1:163216/1‑90 (MQ=255)
caGGGCACCATAGTACGACCACACGGCGGCCCCCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTc < 2:763984/90‑1 (MQ=255)
|
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTC > NZ_CP009273/2345327‑2345500
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCC > NZ_CP009273/2345324‑2345509
|
AGGAACAGCAGCGGCGGAATCCCCCCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAG < SRR3722073.252899/100‑1 (MQ=60)
GAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTA > SRR3722073.692772/1‑100 (MQ=60)
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722073.787636/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722073.686118/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722073.420439/100‑1 (MQ=60)
CGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAC < SRR3722073.159806/100‑1 (MQ=60)
CCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCC > SRR3722073.635146/1‑100 (MQ=60)
ACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACtgtctcttatacacatctgacgctgcc > SRR3722073.305375/1‑73 (MQ=60)
gcgtcagatgtgtataagagacagATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACC < SRR3722073.22268/76‑1 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722073.763923/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722073.312354/1‑100 (MQ=60)
CACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC > SRR3722073.396403/1‑100 (MQ=60)
TGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAAC < SRR3722073.145153/100‑1 (MQ=60)
ACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAG > SRR3722073.475278/1‑100 (MQ=60)
ACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAG < SRR3722073.614862/100‑1 (MQ=60)
ACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAG < SRR3722073.783693/100‑1 (MQ=60)
CACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGT > SRR3722073.78254/1‑100 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC > SRR3722073.216788/1‑100 (MQ=60)
CCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACA < SRR3722073.366071/100‑1 (MQ=60)
TTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGTCCACCCCATCCCCAGGAACCAACGGCGGTGGAACAACAGTACAAGCATCACCTCA > SRR3722073.166483/1‑100 (MQ=60)
CCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCC > SRR3722073.135177/1‑100 (MQ=60)
|
AGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCC > NZ_CP009273/2345324‑2345509
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
