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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,922,863 |
A→G |
V34A (GTC→GCC) |
viaA ← |
ATPase RavA stimulator ViaA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,922,863 | 0 | A | G | 97.6%
| 141.0
/ ‑4.3
| 42 | V34A (GTC→GCC) | viaA | ATPase RavA stimulator ViaA |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (18/23); total (19/23) |
| Fisher's exact test for biased strand distribution p-value = 4.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
CTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCC > NZ_CP009273/3922777‑3922952
|
cTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCg < 1:164050/90‑1 (MQ=255)
ccGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTg < 2:559564/90‑1 (MQ=255)
gACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCg > 2:70448/1‑90 (MQ=255)
gACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCg > 1:635371/1‑90 (MQ=255)
gACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCg > 1:609781/1‑90 (MQ=255)
gACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCg > 2:878738/1‑90 (MQ=255)
tGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTg < 1:251835/90‑1 (MQ=255)
tGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTg < 1:183232/90‑1 (MQ=255)
tGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTg > 2:3527/1‑90 (MQ=255)
cgcAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTg < 2:35916/90‑1 (MQ=255)
gcTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCcagc < 2:591989/90‑1 (MQ=255)
tCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGt > 1:712228/1‑90 (MQ=255)
aGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCgatga > 2:579651/1‑90 (MQ=255)
aGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCgatga > 2:428582/1‑90 (MQ=255)
gggggAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGatc < 2:364804/89‑1 (MQ=255)
gggAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGatcat < 1:626499/90‑1 (MQ=255)
atcatcAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTc > 2:280131/1‑90 (MQ=255)
caccaGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGa < 2:349049/87‑1 (MQ=255)
tcaGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATc > 1:243366/1‑90 (MQ=255)
aGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCaa > 2:564514/1‑90 (MQ=255)
aGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCaa > 1:177275/1‑90 (MQ=255)
gTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAAt < 2:590571/90‑1 (MQ=255)
tGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATc < 1:181639/90‑1 (MQ=255)
gATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGatcat < 2:729899/75‑1 (MQ=255)
gATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGatcat > 1:729899/1‑75 (MQ=255)
gATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATcc > 1:585976/1‑90 (MQ=255)
aTTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATccc > 2:46731/1‑90 (MQ=255)
ttGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCgg > 1:882544/1‑49 (MQ=255)
ttGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCgg < 2:882544/49‑1 (MQ=255)
ccgccTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCtt < 1:479686/90‑1 (MQ=255)
tCAG‑‑GCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGa < 1:184988/90‑1 (MQ=255)
cGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGcc < 1:663913/90‑1 (MQ=255)
cGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGcc < 1:660766/90‑1 (MQ=255)
gTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCa > 1:615559/1‑90 (MQ=255)
gggAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGc > 1:194538/1‑90 (MQ=255)
ggAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCa < 1:401001/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGTCAGCATc < 2:142923/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 2:447160/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 1:636915/90‑1 (MQ=255)
aaTTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATc < 2:71445/90‑1 (MQ=255)
tttttCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATcac > 1:641378/1‑90 (MQ=255)
ttCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACAtt < 1:67189/90‑1 (MQ=255)
aCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATcc < 1:878738/90‑1 (MQ=255)
|
CTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAG‑‑GCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCC > NZ_CP009273/3922777‑3922952
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
TCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCGTTAGCA > NZ_CP009273/3922776‑3922962
|
TCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCG > SRR3722072.620647/1‑100 (MQ=60)
TCTTTCAACCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCG > SRR3722072.646707/1‑100 (MQ=60)
CTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGG < SRR3722072.166905/100‑1 (MQ=60)
TGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAG < SRR3722072.186411/100‑1 (MQ=60)
TGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAG < SRR3722072.256094/100‑1 (MQ=60)
GCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGT > SRR3722072.724920/1‑100 (MQ=60)
GGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATC < SRR3722072.637688/100‑1 (MQ=60)
GGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATC > SRR3722072.247450/1‑100 (MQ=60)
GAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAA > SRR3722072.180346/1‑100 (MQ=60)
CATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCctgtc > SRR3722072.742849/1‑95 (MQ=60)
CATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCC > SRR3722072.596452/1‑100 (MQ=60)
TCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCctgtctcttatacacatctccgagcccacga > SRR3722072.897743/1‑69 (MQ=60)
TGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCT < SRR3722072.184783/100‑1 (MQ=60)
CCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGC < SRR3722072.488391/100‑1 (MQ=60)
GCCTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCA > SRR3722072.626535/1‑100 (MQ=60)
CTTCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGC > SRR3722072.197902/1‑100 (MQ=60)
TCAGGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCAT < SRR3722072.188202/100‑1 (MQ=60)
GGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGctgtctcttatacacatctccgagcccacgagacgtccgattatctcgtat > SRR3722072.436894/1‑49 (MQ=60)
GGCGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCAC > SRR3722072.652818/1‑100 (MQ=60)
CGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACAT < SRR3722072.672562/100‑1 (MQ=60)
CGTGGGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACAT < SRR3722072.675778/100‑1 (MQ=60)
GGAATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAG < SRR3722072.408237/100‑1 (MQ=60)
AATTTTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCG < SRR3722072.648278/100‑1 (MQ=60)
TTTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATC > SRR3722072.779101/1‑100 (MQ=60)
TTCAAAGAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCC < SRR3722072.68445/100‑1 (MQ=60)
GAAGGCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCGTT > SRR3722072.55955/1‑100 (MQ=60)
GCCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCGTTAGCA < SRR3722072.531051/100‑1 (MQ=60)
ACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCGTTAGCA < SRR3722072.893867/100‑1 (MQ=60)
|
TCTTTCAGCCGACTGCGCAGCGCTTCACGCCAGCGGGGAACATCATCAGTGATTGCCGCCTTCAGGCGTGGGAATTTTTCAAAGAAGACCGCCAGCTGCGGTGAGGCCAGCAGTGCGATGATCATCTCTTCGATCAATCCCTCTTCGCTGACGGCCAGCATCACATTAAGCGTATCCAGCGTTAGCA > NZ_CP009273/3922776‑3922962
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
