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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,215,724 |
T→G |
W657G (TGG→GGG) |
metH → |
methionine synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,215,724 | 0 | T | G | 95.7%
| 66.1
/ ‑3.9
| 23 | W657G (TGG→GGG) | metH | methionine synthase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (10/12); total (10/13) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01 |
CGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215639‑4215808
|
cGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGa > 1:183196/1‑90 (MQ=255)
gAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGaa > 2:562311/1‑90 (MQ=255)
aGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAg < 2:141282/90‑1 (MQ=255)
gAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGt > 1:117658/1‑90 (MQ=255)
gCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCt > 2:267821/1‑90 (MQ=255)
ttGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTgg > 1:154686/1‑90 (MQ=255)
tGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGa > 1:284551/1‑90 (MQ=255)
aaTATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGc < 2:546600/90‑1 (MQ=255)
ggCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCaaa < 1:8429/90‑1 (MQ=255)
caAAACCGACGCAACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCAt < 1:69352/90‑1 (MQ=255)
aCCGACGACCCCGCCAACGCCCAGCAGGCGGAGGGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTAcc < 1:481734/90‑1 (MQ=255)
aCCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTAGAATACTCGCTGGTCAAAGGCATTAcc < 2:407097/90‑1 (MQ=255)
acgacACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGt > 2:206385/1‑90 (MQ=255)
cacCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTAt < 1:504051/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 2:154686/90‑1 (MQ=255)
ccAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGc < 2:236741/90‑1 (MQ=255)
caCGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTTAAAGGCATTACCGAGTTTATCGAGCAg < 1:502846/89‑1 (MQ=255)
aaCGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAg < 2:183196/90‑1 (MQ=255)
ccAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGc < 2:202043/53‑1 (MQ=255)
ccAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGc > 1:202043/1‑53 (MQ=255)
cagcagGCGGAGTGGCGCTCGGGGGAAGTGAATaa > 1:449723/1‑35 (MQ=38)
cagcagGCGGAGTGGCGCTCGGGGGAAGTGAATaa < 2:449723/35‑1 (MQ=38)
gcTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCcagc > 1:375720/1‑90 (MQ=255)
|
CGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215639‑4215808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ 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
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215629‑4215808
|
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGA > SRR3722111.185484/1‑100 (MQ=60)
GCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGT > SRR3722111.119137/1‑100 (MQ=60)
TTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGG > SRR3722111.156641/1‑100 (MQ=60)
TACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGA > SRR3722111.288151/1‑100 (MQ=60)
GGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCG < SRR3722111.8534/100‑1 (MQ=60)
CAAAACCGACGCAACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTT < SRR3722111.70170/100‑1 (MQ=60)
ACCGACGACCCCGCCAACGCCCAGCAGGCGGAGGGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCG < SRR3722111.489114/100‑1 (MQ=60)
CACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGAT < SRR3722111.511832/100‑1 (MQ=60)
CCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCtgtctcttatacacatctgacgctgc > SRR3722111.204549/1‑74 (MQ=60)
CGCCAACGCCCAGCAGGCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAActgtctcttatacacatctgacgctgccgacgaatgtcaatgtgt > SRR3722111.456539/1‑55 (MQ=60)
CACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTTAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAG < SRR3722111.510608/100‑1 (MQ=60)
GCGGAGTGGCGCTCGGGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > SRR3722111.381080/1‑100 (MQ=60)
|
ACGATGGCACCGAGCGTTTACTGGAGCTTGCCGAGAAATATCGCGGCAGCAAAACCGACGACACCGCCAACGCCCAGCAGGCGGAGTGGCGCTCGTGGGAAGTGAATAAACGTCTGGAATACTCGCTGGTCAAAGGCATTACCGAGTTTATCGAGCAGGATACCGAAGAAGCCCGCCAGC > NZ_CP009273/4215629‑4215808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
