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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,202,478 |
T→G |
Y345D (TAT→GAT) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,478 | 0 | T | G | 94.1%
| 48.6
/ ‑3.8
| 17 | Y345D (TAT→GAT) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (9/7); total (9/8) |
| Fisher's exact test for biased strand distribution p-value = 4.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTT > NZ_CP009273/2202402‑2202561
|
tCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 1:421890/90‑1 (MQ=255)
gAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCa < 2:525316/90‑1 (MQ=255)
aGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 1:255380/90‑1 (MQ=255)
aGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 2:213410/90‑1 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTg > 2:27337/1‑90 (MQ=255)
tgtgtCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTg > 2:506331/1‑90 (MQ=255)
gagCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGt > 2:485682/1‑90 (MQ=255)
agCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc > 1:524655/1‑79 (MQ=255)
agCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 2:524655/79‑1 (MQ=255)
gCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 1:510647/75‑1 (MQ=255)
gCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc > 2:510647/1‑75 (MQ=255)
gCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAgc > 2:64354/1‑90 (MQ=255)
cTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATg < 2:343417/90‑1 (MQ=255)
tGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGa > 1:294185/1‑90 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 1:308351/1‑90 (MQ=255)
gCAACACCTTGCTATGCCCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcatca < 1:197853/90‑1 (MQ=255)
ccTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCtt > 1:258498/1‑90 (MQ=255)
|
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTT > NZ_CP009273/2202402‑2202561
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGA > NZ_CP009273/2202402‑2202566
|
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCTCAGGCG < SRR3722111.428135/100‑1 (MQ=60)
gacagGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGT < SRR3722111.518567/95‑1 (MQ=60)
AGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGT < SRR3722111.258385/100‑1 (MQ=60)
GTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTC > SRR3722111.532865/1‑100 (MQ=60)
GTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGA > SRR3722111.297956/1‑100 (MQ=60)
nnnnnnnnnnnnnnnnnnnntagccCCGCAACCCCTTGCGATGCCCGCGATACGGCCCAGGAGCTGGTTAATGTCGGCGCACAAATAGCCGCCATNNNNC < SRR3722111.449107/75‑1 (MQ=60)
CTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > SRR3722111.312375/1‑100 (MQ=60)
CACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTT > SRR3722111.261541/1‑100 (MQ=60)
GCAACACCTTGCTATGCCCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGG < SRR3722111.200313/100‑1 (MQ=60)
CAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGA > SRR3722111.22210/1‑100 (MQ=60)
|
TCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGCGGA > NZ_CP009273/2202402‑2202566
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
