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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,901,121 |
A→G |
D202D (GAT→GAC) |
pstB ← |
phosphate ABC transporter ATP‑binding protein PstB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,901,121 | 0 | A | G | 100.0%
| 47.6
/ NA
| 15 | D202D (GAT→GAC) | pstB | phosphate ABC transporter ATP‑binding protein PstB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (5/10); total (5/10) |
TCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAATCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGGTTCGTCGAGCA > NZ_CP009273/3901041‑3901200
|
tCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTc < 2:180514/90‑1 (MQ=255)
tCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGATGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTc < 2:223191/90‑1 (MQ=255)
aGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCg > 1:249065/1‑90 (MQ=255)
aaCGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGc < 2:332480/90‑1 (MQ=255)
gCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGctct < 1:349771/90‑1 (MQ=255)
gtgtGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCa > 1:83318/1‑90 (MQ=255)
tgGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATa < 2:333508/90‑1 (MQ=255)
cGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGcc < 2:255894/90‑1 (MQ=255)
caacGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTa < 1:119147/90‑1 (MQ=255)
aacGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTag > 2:61983/1‑90 (MQ=255)
gtgGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAaca > 2:254208/1‑90 (MQ=255)
ggTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGACGAACACgg > 1:207132/1‑90 (MQ=255)
gATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGGTtcgtc < 2:83318/90‑1 (MQ=255)
accacGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGGTTCGTCGagc < 2:43335/90‑1 (MQ=255)
ccacGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGGTTCGTCGagca < 2:181229/90‑1 (MQ=255)
|
TCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAATCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGGTTCGTCGAGCA > NZ_CP009273/3901041‑3901200
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
ACTCAATCAATTCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAATCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGG > NZ_CP009273/3901030‑3901189
|
ACTCAATCAATTCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTT < SRR3722116.229284/100‑1 (MQ=60)
CAATTCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCG > SRR3722116.252564/1‑100 (MQ=60)
CATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCA > SRR3722116.84353/1‑100 (MQ=60)
GCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCC < SRR3722116.354980/100‑1 (MQ=60)
GAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTgtctcttatacacatctgacgctgccgacgaagttggctgtg > SRR3722116.331470/1‑58 (MQ=60)
CAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGT < SRR3722116.120580/100‑1 (MQ=60)
GCATGTTGTGGGTGACGATCACCACGGTGTAGTCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGACGAACACGG > SRR3722116.209764/1‑100 (MQ=60)
|
ACTCAATCAATTCGCCCAGGTACATAAACGCCGTGTGGTCGGAACAACGCGCAGCCTGCTGCATGTTGTGGGTGACGATCACCACGGTGTAATCCTGCTTCAGTTCGGTGATCAGCTCTTCAATACGCCCGGTAGAGATAGGGTCGAGCGCCGAACACGG > NZ_CP009273/3901030‑3901189
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
