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 |
A2 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
RA |
NZ_CP009273 |
490,029 |
T→G |
C57G (TGC→GGC) |
recR → |
recombination mediator RecR |
|
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
* | NZ_CP009273 | 490,029 | 0 | T | G | 95.0%
| 47.7
/ ‑6.2
| 20 | C57G (TGC→GGC) | recR | recombination mediator RecR |
Reads supporting (aligned to +/- strand): ref base T (0/0); major base G (11/8); minor base C (1/0); total (12/8) |
Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01 |
CACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTTTT > NZ_CP009273/489898‑490164
|
cACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCCGGCGCTCACCCGGGCGGTGTTGGGAATCGGCCACGGCGCCGa > 2:271276/1‑139 (MQ=255)
cACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCCCACCCCGGCGATGTCGGGAATACGCCACCGCGcccc > 2:349852/1‑137 (MQ=255)
cgcTGTCTGCCGGGCGTTGGCCCGAAGTTGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCCCCCGGGCGATGTCGGGAATCGGCCACGGCGCCGGGTGcc > 2:452148/1‑139 (MQ=255)
cTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCCGGGGCCGGCGCTCACCCGGGCGGTGTCGGGAAACGGCCACGGCGCCGCTTGCCGCACtt > 2:145900/1‑139 (MQ=255)
cgcAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGAGGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGGAATTCGCCACGGCGCCGGGTGCCGCACTTTCCACGCACAGGAGGTCTggtacaa > 2:528789/1‑133 (MQ=255)
tCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCCGGCGCTCACCCCGGCGGTGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCcgcg > 1:356926/1‑139 (MQ=255)
tCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCcccg > 1:508798/1‑139 (MQ=255)
aGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGaaa < 2:508798/138‑1 (MQ=255)
gTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAAt < 1:528789/139‑1 (MQ=255)
gcAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCcggcg < 2:356926/139‑1 (MQ=255)
aCCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACg < 1:452148/139‑1 (MQ=255)
gggCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCAt > 1:195593/1‑139 (MQ=255)
ggCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGt < 2:330485/97‑1 (MQ=255)
ggCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGt > 1:330485/1‑97 (MQ=255)
ggCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCt > 1:350964/1‑104 (MQ=255)
ggCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCt < 2:350964/104‑1 (MQ=255)
tGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAg > 2:185043/1‑137 (MQ=255)
ggCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGa > 1:572810/1‑130 (MQ=255)
ggCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGa < 2:572810/130‑1 (MQ=255)
cACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGtttt < 1:349852/139‑1 (MQ=255)
|
CACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTTTT > NZ_CP009273/489898‑490164
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TATGGAAGCACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTTTTCAGGTCGTTAT > NZ_CP009273/489890‑490175
|
TATGGAAGCACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATT < SRR3722139.110585/149‑1 (MQ=60)
GCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCCGGCGCTCACCCCGGCGGTGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGT > SRR3722139.361238/1‑151 (MQ=60)
GCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCCGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCCCTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCccgg > SRR3722139.514665/1‑147 (MQ=60)
CGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGG < SRR3722139.534875/151‑1 (MQ=60)
GGCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATT > SRR3722139.198002/1‑151 (MQ=60)
GCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTctgtctcttatacacatctccgagcccacg > SRR3722139.334544/1‑119 (MQ=60)
GCGCTCACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGGCAAATCTGCGTGGTGGAGctgtctcttatacacatctccgagc > SRR3722139.355207/1‑126 (MQ=60)
CACCCGGGCGATGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAG < SRR3722139.457437/151‑1 (MQ=60)
TGTCGGAAATCGGCCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTT > SRR3722139.579359/1‑151 (MQ=60)
CCACGGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTTTTCAGGTCGTTAT < SRR3722139.354084/151‑1 (MQ=60)
|
TATGGAAGCACTGCGCTGTCTGCCGGGCGTTGGCCCGAAGTCGGCGCAGCGTATGGCGTTCACGCTGCTTCAGCGCGATCGTAGCGGCGGGATGCGTCTGGCGCAGGCGCTCACCCGGGCGATGTCGGAAATCGGCCACTGCGCCGATTGCCGCACTTTCACCGAACAGGAAGTCTGTAACATCTGTTCGAATCCGCGTCGTCAGGAAAACGGTCAAATCTGCGTGGTGGAGAGTCCGGCGGACATCTACGCCATTGAGCAGACGGGGCAGTTTTCAGGTCGTTAT > NZ_CP009273/489890‑490175
|
Alignment Legend |
---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |