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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
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 | 93.3%
| 43.1
/ NA
| 15 | H147P (CAC→CCC) | glpT | glycerol‑3‑phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (7/7); total (7/8) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAA > NZ_CP009273/2345337‑2345483
|
gcggAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTAc < 1:447760/90‑1 (MQ=255)
accaccGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg < 2:169774/90‑1 (MQ=255)
gACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCa > 1:270729/1‑90 (MQ=255)
gTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCAccc < 1:345978/90‑1 (MQ=255)
gTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg > 1:193604/1‑69 (MQ=255)
gTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg < 2:193604/69‑1 (MQ=255)
cTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGc > 1:223178/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg > 1:217173/1‑59 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACAcgg < 2:217173/59‑1 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:181177/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:230127/1‑90 (MQ=255)
gACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCag > 1:257343/1‑90 (MQ=255)
caATGCCTCCCCGTTCTTTCTCCCCCCCCCAGTGCACCATAGTACGACCACACGGCGGCCCCCCCATCCCCTGGACCCAACCGCAGAGGa < 1:62529/90‑1 (MQ=255)
caATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGa < 1:71699/90‑1 (MQ=255)
gTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACaa < 2:442377/90‑1 (MQ=255)
|
GCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAA > NZ_CP009273/2345337‑2345483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCCCAT > NZ_CP009273/2345316‑2345512
|
TCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGG < SRR3722094.110940/100‑1 (MQ=60)
CCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGC < SRR3722094.52423/100‑1 (MQ=60)
GCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGG < SRR3722094.455638/100‑1 (MQ=60)
TACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCA > SRR3722094.274765/1‑100 (MQ=60)
GTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGG < SRR3722094.351712/100‑1 (MQ=60)
TGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCctgtctcttat > SRR3722094.196244/1‑89 (MQ=60)
CAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGC > SRR3722094.226170/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCctgtctcttatacacatctga > SRR3722094.220104/1‑79 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722094.183665/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722094.233305/1‑100 (MQ=60)
GTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAG > SRR3722094.261146/1‑100 (MQ=60)
CAATGCCTCCCCGTTCTTTCTCCCCCCCCCAGTGCACCATAGTACGACCACACGGCGGCCCCCCCATCCCCTGGACCCAACCGCAGAGGAACAACAGTAC < SRR3722094.63404/100‑1 (MQ=60)
CAATGCCGCCACGTTCTTTCTGCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTAC < SRR3722094.72709/100‑1 (MQ=60)
GCGACCACCAGGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGA > SRR3722094.500550/1‑100 (MQ=60)
GGGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCCCAT > SRR3722094.266389/1‑100 (MQ=60)
|
TCCCCAGCAGGAACAGCAGCGGCGGAATACCACCACCGACGTTGTGCGCACAGTTCCACACTGACACAATGCCGCCACGTTCTTTCTGCGACCACCAGTGCACCATAGTACGACCACACGGCGGCCACCCCATCCCCTGGAACCAACCGCAGAGGAACAACAGTACAAACATCACCGCAATGCTCGACGTCGCCCAT > NZ_CP009273/2345316‑2345512
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
