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 F3 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,807,028 |
T→C |
E121G (GAA→GGA) |
BW25113_RS09050 ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,807,028 | 0 | T | C | 96.3%
| 83.4
/ ‑3.4
| 27 | E121G (GAA→GGA) | BW25113_RS09050 | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (14/12); total (15/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.72e-01 |
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806947‑1807108
|
atataATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 2:523229/90‑1 (MQ=255)
gTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCa > 1:331963/1‑90 (MQ=255)
tCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCaa > 2:893086/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa < 1:539228/71‑1 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGa > 2:539228/1‑71 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTg < 2:151072/75‑1 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTg > 1:151072/1‑75 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTcc < 1:381468/86‑1 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTcc > 2:381468/1‑86 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:864450/1‑90 (MQ=255)
cTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATa > 1:964764/1‑90 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa < 2:976869/61‑1 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGa > 1:976869/1‑61 (MQ=255)
tAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATaaa > 2:221640/1‑90 (MQ=255)
tGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGc > 1:777803/1‑52 (MQ=255)
tGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGc < 2:777803/52‑1 (MQ=255)
tGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCttta < 2:864450/90‑1 (MQ=255)
tAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCtttattta > 2:961006/1‑90 (MQ=255)
gTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTAt > 1:935/1‑90 (MQ=255)
tGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCAc < 2:389925/90‑1 (MQ=255)
gATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACt < 2:908064/90‑1 (MQ=255)
aaTTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAt > 1:606716/1‑90 (MQ=255)
ttGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATaa < 2:606716/90‑1 (MQ=255)
tGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATaaa < 2:964764/90‑1 (MQ=255)
gTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGa > 1:759407/1‑90 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATAcc > 2:235587/1‑62 (MQ=255)
gTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATAcc < 1:235587/62‑1 (MQ=255)
|
ATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806947‑1807108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GATGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806942‑1807108
|
ctacacctaagccttcgtcggcagcgtcagatgtgtataagagacagACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATAC < SRR3722236.311266/53‑1 (MQ=60)
aagagacagGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCC < SRR3722236.547516/91‑1 (MQ=60)
ATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCA > SRR3722236.336702/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCtgtc > SRR3722236.153274/1‑96 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722236.879614/1‑100 (MQ=60)
GTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATA > SRR3722236.981781/1‑100 (MQ=60)
ATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGctgtctcttatacacatct > SRR3722236.994091/1‑81 (MQ=60)
AGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCT < SRR3722236.386828/100‑1 (MQ=60)
CCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGActgtctcttatacacatctgacgctgcc > SRR3722236.791211/1‑72 (MQ=60)
TAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTAT > SRR3722236.950/1‑100 (MQ=60)
gatgtgtataagagacagGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGA < SRR3722236.239096/82‑1 (MQ=60)
ATACTGATCAAATTGGTCATTTTTCCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCAT > SRR3722236.616391/1‑100 (MQ=60)
GATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > SRR3722236.772466/1‑100 (MQ=60)
|
GATGTATATAATTTTGTTCATAGTATATAGTCCTTAAATAGTGAATAACCAACCTGTTTTTTATACTGATCAAATTGGTCATTTTTTCTGGGCGAAATACAGAAGTGACATCCATTCCAATAAAATCTTTATTTATACCTCTTATCCGAATTTCACTACCATAAAGA > NZ_CP009273/1806942‑1807108
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
