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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
448,331 |
G→T |
A224D (GCC→GAC) |
ampG ← |
muropeptide MFS transporter AmpG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 448,331 | 0 | G | T | 92.3%
| 80.1
/ 0.8
| 26 | A224D (GCC→GAC) | ampG | muropeptide MFS transporter AmpG |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base T (11/13); total (12/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.97e-01 |
ACGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTT > NZ_CP009273/448244‑448411
|
aCGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCa > 1:257633/1‑90 (MQ=255)
aaCGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAg < 2:455490/90‑1 (MQ=255)
aCGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGa < 1:586786/90‑1 (MQ=255)
gTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGc < 2:344822/90‑1 (MQ=255)
gTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGc < 1:658691/90‑1 (MQ=255)
cGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGcaacaa < 2:891807/90‑1 (MQ=255)
cGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCtt < 2:375664/90‑1 (MQ=255)
cAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAg < 2:75419/90‑1 (MQ=255)
cAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAg < 2:423585/90‑1 (MQ=255)
gCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCg > 2:49186/1‑90 (MQ=255)
aGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGc > 1:830006/1‑90 (MQ=255)
aGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGGGCAACAACCGCTTGTTCCAGCGTTTTGGGc > 1:47419/1‑90 (MQ=255)
gCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGca > 2:751657/1‑90 (MQ=255)
cACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGcac > 1:764922/1‑90 (MQ=255)
cACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGcac > 1:382982/1‑90 (MQ=255)
cACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGcac > 2:544201/1‑90 (MQ=255)
cACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGcac < 2:358266/90‑1 (MQ=255)
cACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGCGCAACAACCGCTTGTTCCAGCGTTTTGGGcac > 2:421969/1‑90 (MQ=255)
aCGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGcaca < 1:584050/90‑1 (MQ=255)
aTAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGa > 2:300824/1‑90 (MQ=255)
tAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGaa < 2:341013/90‑1 (MQ=255)
gCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGgtgt < 1:702708/90‑1 (MQ=255)
aaaaTAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCg > 2:154430/1‑90 (MQ=255)
aTAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCggtt < 2:830006/90‑1 (MQ=255)
aGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAg > 1:816028/1‑59 (MQ=255)
aGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAg < 2:816028/59‑1 (MQ=255)
|
ACGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTT > NZ_CP009273/448244‑448411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ATCAAACCCGACGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTTGGTTCTGG > NZ_CP009273/448234‑448419
|
ATCAAACCCGACGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCA > SRR3722072.262001/1‑100 (MQ=60)
ACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAG < SRR3722072.597271/100‑1 (MQ=60)
GTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAA < SRR3722072.670448/100‑1 (MQ=60)
CAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGC > SRR3722072.844410/1‑100 (MQ=60)
CAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGGGCAACAACCGCTTGTTCCAGCGTTTTGGGC > SRR3722072.48284/1‑100 (MQ=60)
GCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCAC > SRR3722072.389828/1‑100 (MQ=60)
GCTTATACAGCACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCAC > SRR3722072.778401/1‑100 (MQ=60)
ACGATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGT < SRR3722072.594492/100‑1 (MQ=60)
ATAAGAAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGG > SRR3722072.747176/1‑100 (MQ=60)
AAGCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCctgtctcttatacacatctcc > SRR3722072.830240/1‑79 (MQ=60)
GCAAAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTTGGTTC < SRR3722072.715249/100‑1 (MQ=60)
AAATAAGCCAGTCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTTGGTTCTGG > SRR3722072.431593/1‑100 (MQ=60)
|
ATCAAACCCGACGCCGCGAATCAAAAACGTGGTTGTCAGGCTCATGGCGAATGCGTCGCCCAGCTTATACAGCACGATAAGAAGCAAAATAAGCCAGGCATTATTGCGACCAAAGAAATCTCGCAGAGGTGCAACAACCGCTTGTTCCAGCGTTTTGGGCACAGGAATGGTGTCGGTTGGTTCTGG > NZ_CP009273/448234‑448419
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
