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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 52.4
/ NA
| 17 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (3/14); total (3/14) |
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTC > NZ_CP009273/2345327‑2345500
|
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:561457/90‑1 (MQ=255)
aaCAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 2:27009/90‑1 (MQ=255)
agcagcGGCGGAATACCACCCCCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:440104/90‑1 (MQ=255)
agcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCAcc < 1:99661/90‑1 (MQ=255)
gcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc < 1:237556/86‑1 (MQ=255)
gcagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGc > 2:237556/1‑86 (MQ=255)
cagcGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCAt < 2:499731/90‑1 (MQ=255)
gcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAc < 2:545249/90‑1 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 1:96158/90‑1 (MQ=255)
gtgCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCAt < 1:243/90‑1 (MQ=255)
cacTGACCCAACGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGaaccaacc < 1:268514/90‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:86098/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:102073/1‑90 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 2:172362/90‑1 (MQ=255)
ccgccACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGaacaac < 2:424379/90‑1 (MQ=255)
ctGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCAc < 2:402254/90‑1 (MQ=255)
caGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTc < 2:457695/90‑1 (MQ=255)
|
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTC > NZ_CP009273/2345327‑2345500
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
AGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC > NZ_CP009273/2345324‑2345473
|
AGGAACAGCAGCGGCGGAATCCCCCCCCCGACGTTGTGCGCACAGTTCCACACTGATACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAG < SRR3722092.441644/100‑1 (MQ=60)
AACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAC < SRR3722092.241424/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCCCCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722092.448735/100‑1 (MQ=60)
AGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGAC < SRR3722092.101364/100‑1 (MQ=60)
GTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAAC < SRR3722092.251/100‑1 (MQ=60)
GTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAAC < SRR3722092.97808/100‑1 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722092.103816/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722092.87572/1‑100 (MQ=60)
CACTGACCCAACGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC < SRR3722092.273011/100‑1 (MQ=60)
|
AGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAAC > NZ_CP009273/2345324‑2345473
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
