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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,284,519 |
T→C |
S181P (TCC→CCC) |
narP → |
nitrate/nitrite response regulator protein NarP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,284,519 | 0 | T | C | 92.9%
| 35.8
/ ‑6.2
| 14 | S181P (TCC→CCC) | narP | nitrate/nitrite response regulator protein NarP |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (9/4); total (9/5) |
| Fisher's exact test for biased strand distribution p-value = 3.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTT > NZ_CP009273/2284435‑2284601
|
gTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAg > 2:145542/1‑90 (MQ=255)
aCGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACa < 1:145542/90‑1 (MQ=255)
tGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATc > 2:364254/1‑90 (MQ=255)
cTGGCACAGCGGCTGTCAAATAAACAGATTGCCTCGGTGTTGCATAGTCCCGAGCCGACAGTAAAAGTACATATTCGCAATCTGCCGCGt < 1:537672/90‑1 (MQ=255)
ggCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTaa < 1:81154/90‑1 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 1:515298/1‑90 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 2:250376/1‑90 (MQ=255)
ggggCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCaa > 2:275010/1‑90 (MQ=255)
tGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTcc > 1:12321/1‑90 (MQ=255)
tGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTcc > 2:157511/1‑90 (MQ=255)
tCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGc < 2:12956/90‑1 (MQ=255)
tGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTggcggc > 2:123064/1‑90 (MQ=255)
cGGGGTTGAATCTTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCCCACGCGTGGCGGccacca < 1:408554/90‑1 (MQ=255)
gAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGtt > 2:463600/1‑90 (MQ=255)
|
GTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTT > NZ_CP009273/2284435‑2284601
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 29 ≤ 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
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCT > NZ_CP009273/2284426‑2284604
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGC < SRR3722109.388013/100‑1 (MQ=60)
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGC < SRR3722109.522905/100‑1 (MQ=60)
ACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTAC < SRR3722109.147341/100‑1 (MQ=60)
AGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAA > SRR3722109.523126/1‑100 (MQ=60)
CTGGCACAGCGGCTGTCAAATAAACAGATTGCCTCGGTGTTGCATAGTCCCGAGCCGACAGTAAAAGTACATATTCGCAATCTGCCGCGTAAACTCAAGG < SRR3722109.545849/100‑1 (MQ=60)
GGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTC < SRR3722109.82151/100‑1 (MQ=60)
GCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCC > SRR3722109.12495/1‑100 (MQ=60)
tcggcagcgtcagatgtgtataagagacagGAATATTCCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGC < SRR3722109.392981/70‑1 (MQ=60)
CGGGGTTGAATCTTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCCCACGCGTGGCGGCCACCATTCTGTTCCC < SRR3722109.414506/100‑1 (MQ=60)
|
CCCTTCAGCGTGCTGACGGAGCGCGAGCTGGATGTTCTGCACGAGCTGGCACAGGGGCTGTCAAATAAACAGATTGCCTCGGTGTTGAATATTTCCGAGCAGACAGTAAAAGTACATATTCGCAATCTGCTGCGTAAACTCAATGTCCGCTCACGCGTGGCGGCCACCATTCTGTTCCT > NZ_CP009273/2284426‑2284604
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
