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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
886,189 |
A→G |
G7G (GGT→GGC) |
grxA ← |
glutaredoxin 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 886,189 | 0 | A | G | 95.8%
| 69.7
/ ‑3.4
| 24 | G7G (GGT→GGC) | grxA | glutaredoxin 1 |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (13/10); total (14/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886106‑886270
|
tactgatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCaaaa > 1:489726/1‑90 (MQ=255)
ctgatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAAt > 2:368251/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 2:381921/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 1:486838/1‑90 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa < 2:295133/90‑1 (MQ=255)
gatactgaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATaa > 2:144703/1‑90 (MQ=255)
gaAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGttt < 2:439582/90‑1 (MQ=255)
tcGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCattatt > 2:90844/1‑90 (MQ=255)
tCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTtctctc < 1:144703/90‑1 (MQ=255)
tttCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGAttt < 2:50581/90‑1 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCattatt > 1:426548/1‑69 (MQ=255)
tcAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCattatt < 2:426548/69‑1 (MQ=255)
gCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTtctc > 1:52292/1‑70 (MQ=255)
gCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTtctc < 2:52292/70‑1 (MQ=255)
gATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGttt > 2:200023/1‑54 (MQ=255)
gATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGttt < 1:200023/54‑1 (MQ=255)
gcacgcacACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGc < 2:489726/90‑1 (MQ=255)
gggCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCt > 2:346192/1‑90 (MQ=255)
gggCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCt > 2:501378/1‑90 (MQ=255)
ggCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTg < 2:482347/90‑1 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 2:141801/1‑90 (MQ=255)
aaCCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGaaa > 2:61204/1‑90 (MQ=255)
cccGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGt < 2:350437/90‑1 (MQ=255)
cccGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGt > 1:144697/1‑90 (MQ=255)
|
TACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886106‑886270
|
| 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
AATATCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886096‑886270
|
AATATCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAA > SRR3722114.495852/1‑100 (MQ=60)
TCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAA > SRR3722114.492933/1‑100 (MQ=60)
TACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATctgtctct > SRR3722114.146387/1‑92 (MQ=60)
ggctcggagatgtgtataagagacagTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTC < SRR3722114.201974/74‑1 (MQ=60)
TCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATT < SRR3722114.146183/100‑1 (MQ=60)
GCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCActgtctcttat > SRR3722114.431802/1‑89 (MQ=60)
CAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGActgtctctta > SRR3722114.52817/1‑90 (MQ=60)
GTAAGGGCAACCCGAACGGCCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > SRR3722114.146177/1‑100 (MQ=60)
|
AATATCTACATACTGATACTGAAAATCATCGCGTTCATTGCTCAATTTCTCAGCCAGATCTTTTGCACGCACACAGTAAGGGCAACCCGAACGACCAAAAATAACGGTTTGCATTATTTCTCTCCTCATAGATTTATGCCTGTAATGATCACGCTAAAATGTATTCGCTGAAAGT > NZ_CP009273/886096‑886270
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
