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 |
2,202,478 |
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 | 100.0%
| 36.9
/ NA
| 13 | Y345D (TAT→GAT) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/5); total (8/5) |
GACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > NZ_CP009273/2202396‑2202553
|
gACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACcg > 1:343404/1‑90 (MQ=255)
gACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACcg > 1:96960/1‑90 (MQ=255)
tCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATAc < 2:178835/90‑1 (MQ=255)
gAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCa < 1:58874/90‑1 (MQ=255)
aaaaGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAgg > 2:43453/1‑90 (MQ=255)
aGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 1:285447/90‑1 (MQ=255)
gCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc > 1:149759/1‑65 (MQ=255)
gCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGgcgc < 2:149759/65‑1 (MQ=255)
gCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTgg > 2:448051/1‑90 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 1:435712/1‑90 (MQ=255)
ccGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGcat > 2:215346/1‑90 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAg > 1:57390/1‑53 (MQ=255)
ttGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAg < 2:57390/53‑1 (MQ=255)
|
GACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > NZ_CP009273/2202396‑2202553
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ 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
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202380‑2202563
|
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGA < SRR3722094.114522/100‑1 (MQ=60)
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGA < SRR3722094.509150/100‑1 (MQ=60)
CATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCG > SRR3722094.349089/1‑100 (MQ=60)
CATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCG > SRR3722094.98364/1‑100 (MQ=60)
GAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTT < SRR3722094.59697/100‑1 (MQ=60)
AGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGT < SRR3722094.289739/100‑1 (MQ=60)
GCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCtgtctcttatacac > SRR3722094.151854/1‑86 (MQ=60)
CTCGATAGCACCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCAT > SRR3722094.443323/1‑100 (MQ=60)
CCGCAACACCTTGCGATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACctgtctcttatacacatctgacgctgc > SRR3722094.58185/1‑73 (MQ=60)
|
GTTCATCATCATTACTGACGCATCAGGTGAAAAAGTGTGTCCAGAGCGGCATCAAAGTGCTGGGACTGGCAGCGCTCGATAGCACCGCAACACCTTGCTATGACCGCGATACGGCCCAGGCGCTGGTTAATGTCGGCGCACAAATAGCCGCCATGACGCCGGGCGAGCTGGCATCATGGCTTGC > NZ_CP009273/2202380‑2202563
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
