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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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 | 100.0%
| 56.6
/ NA
| 18 | D18G (GAT→GGT) | yibB | protein YibB |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (6/12); total (6/12) |
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAA > NZ_CP009273/3786906‑3787071
|
aaGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACcccc < 1:341617/90‑1 (MQ=255)
aaGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACcccc > 1:451238/1‑90 (MQ=255)
gTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCctc < 2:135964/90‑1 (MQ=255)
ggCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTAcc < 2:430702/90‑1 (MQ=255)
ggCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTAcc > 2:111606/1‑90 (MQ=255)
tCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCaaaa < 2:451238/90‑1 (MQ=255)
cAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAat > 1:214132/1‑90 (MQ=255)
cTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTg < 1:506393/90‑1 (MQ=255)
aGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCAt > 2:487212/1‑90 (MQ=255)
cTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa < 1:487212/90‑1 (MQ=255)
cTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa < 2:180727/90‑1 (MQ=255)
tAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTAc < 1:550036/90‑1 (MQ=255)
tttCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACtaata < 2:532366/90‑1 (MQ=255)
ttCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACtaataa < 2:334076/90‑1 (MQ=255)
tCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAg < 1:392337/90‑1 (MQ=255)
ggAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa > 2:363391/1‑78 (MQ=255)
ggAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTa < 1:363391/78‑1 (MQ=255)
gCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATaaaaaaa > 1:147050/1‑90 (MQ=255)
|
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAA > NZ_CP009273/3786906‑3787071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ 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
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAA > NZ_CP009273/3786894‑3787071
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCC < SRR3722092.118197/100‑1 (MQ=60)
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCC < SRR3722092.278331/100‑1 (MQ=60)
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCC < SRR3722092.456984/100‑1 (MQ=60)
TCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCC > SRR3722092.460140/1‑100 (MQ=60)
AAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATG < SRR3722092.347712/100‑1 (MQ=60)
GCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAAT > SRR3722092.217661/1‑100 (MQ=60)
CTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGG < SRR3722092.516517/100‑1 (MQ=60)
agAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGAC < SRR3722092.370145/98‑1 (MQ=60)
CTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGAC < SRR3722092.496894/100‑1 (MQ=60)
TAGTTTTTCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACC < SRR3722092.561081/100‑1 (MQ=60)
TCACGGAACCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATA < SRR3722092.399838/100‑1 (MQ=60)
CCCTTTATTAGCAGTCCAACCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAA > SRR3722092.149526/1‑100 (MQ=60)
|
CATCTCATTTTCAAGTGCGGCCAGACGCTCAAAGTAACTAAAATAAACATCAACTGAACGAGCTAGTTTTTCACGGAACCCTTTATTAGCAGTCCAATCCCCTCTACCAATGTCAAAATATGCAGTGATAATTGTGGTGGATGATTTCATTACTAATAAGACCATTAATATAAAAAAA > NZ_CP009273/3786894‑3787071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
