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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,786,991 |
T→C |
D18G (GAT→GGT) |
yibB ← |
protein YibB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,786,991 | 0 | T | C | 89.5%
| 45.1
/ ‑0.9
| 19 | D18G (GAT→GGT) | yibB | protein YibB |
| Reads supporting (aligned to +/- strand): ref base T (0/2); new base C (8/9); total (8/11) |
| Fisher's exact test for biased strand distribution p-value = 4.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.20e-01 |
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786906‑3787073
|
aaGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACcccc < 1:462304/90‑1 (MQ=255)
cGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCa < 1:265580/90‑1 (MQ=255)
tAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCa < 2:169554/90‑1 (MQ=255)
aaCTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAg > 1:600514/1‑90 (MQ=255)
aaCTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAg > 1:625053/1‑90 (MQ=255)
cTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTg > 1:529352/1‑90 (MQ=255)
cTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGgatg < 1:750406/90‑1 (MQ=255)
cTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGgatg < 2:131225/90‑1 (MQ=255)
tGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGgatga > 1:605528/1‑90 (MQ=255)
tGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGgatga > 1:619214/1‑90 (MQ=255)
aCGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGAttt > 1:609474/1‑90 (MQ=255)
aGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCAt < 2:140408/90‑1 (MQ=255)
aGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTC‑AAATATGCAGTGATAATTGTGGTGGATGATTTCAtt > 2:472068/1‑90 (MQ=255)
cTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa < 2:697477/90‑1 (MQ=255)
cTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa < 2:619214/90‑1 (MQ=255)
tttCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACtaata < 1:680129/90‑1 (MQ=255)
cACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGa < 2:289926/90‑1 (MQ=255)
ttattaGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAAtata < 2:83863/90‑1 (MQ=255)
aGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGa > 1:150611/1‑90 (MQ=255)
|
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > NZ_CP009273/3786906‑3787073
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGAATTATATCATA > NZ_CP009273/3786894‑3787084
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCC < SRR3722079.462903/100‑1 (MQ=60)
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACC < SRR3722079.292929/100‑1 (MQ=60)
TTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACC < SRR3722079.518312/100‑1 (MQ=60)
TTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCA < SRR3722079.173514/100‑1 (MQ=60)
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATG < SRR3722079.466350/100‑1 (MQ=60)
CGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAG > SRR3722079.631428/1‑100 (MQ=60)
CGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAG < SRR3722079.267806/100‑1 (MQ=60)
CGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAG > SRR3722079.606561/1‑100 (MQ=60)
CTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTG > SRR3722079.534280/1‑100 (MQ=60)
AAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGA > SRR3722079.611633/1‑100 (MQ=60)
AAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGA > SRR3722079.625509/1‑100 (MQ=60)
CATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTT > SRR3722079.615636/1‑100 (MQ=60)
CTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTAC < SRR3722079.758424/100‑1 (MQ=60)
TTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAA < SRR3722079.687269/100‑1 (MQ=60)
CTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGA > SRR3722079.151911/1‑100 (MQ=60)
GTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGAATTATATCATA > SRR3722079.679001/1‑100 (MQ=60)
GTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGAATTATATCATA > SRR3722079.174276/1‑100 (MQ=60)
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAAGAATTATATCATA > NZ_CP009273/3786894‑3787084
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
