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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,306,692 |
A→T |
I115N (ATC→AAC) |
phnM ← |
alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,306,692 | 0 | A | T | 83.3%
| 80.9
/ 5.0
| 32 | I115N (ATC→AAC) | phnM | alpha‑D‑ribose 1‑methylphosphonate 5‑triphosphate diphosphatase |
| Reads supporting (aligned to +/- strand): ref base A (3/2); new base T (10/15); total (15/17) |
| Fisher's exact test for biased strand distribution p-value = 6.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306605‑4306777
|
gtggtgTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGttc > 2:305242/1‑90 (MQ=255)
aTGCGTCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGGGGGGTTGGCGGGGGGGTTTGGCGTCCCTTCGGTGGCGTTGGTCGTCTgctc > 2:548157/1‑90 (MQ=255)
aTGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTtctc > 1:604114/1‑90 (MQ=255)
gCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCa > 2:111333/1‑90 (MQ=255)
cGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAg < 2:544536/90‑1 (MQ=255)
gCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGAt > 2:759297/1‑90 (MQ=255)
gCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGAt > 1:762566/1‑90 (MQ=255)
gCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGGCTCTTCGATGGCGTTGATCATCTTCTCCAGAt > 2:370598/1‑90 (MQ=255)
aGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATtc > 2:698727/1‑90 (MQ=255)
cagATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATc > 1:477981/1‑90 (MQ=255)
gCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATcgccgc < 2:604114/90‑1 (MQ=255)
cGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTcg < 2:589250/90‑1 (MQ=255)
gTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTcgcg > 2:318828/1‑90 (MQ=255)
gTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTcgcg > 1:832776/1‑90 (MQ=255)
gCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCa > 2:236530/1‑90 (MQ=255)
ggCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTc < 2:828221/90‑1 (MQ=255)
cgcgGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGc > 2:629875/1‑90 (MQ=255)
cgcgGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGc > 2:93238/1‑90 (MQ=255)
cgGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCa < 1:75698/90‑1 (MQ=255)
cgGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGCTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCa > 1:637669/1‑90 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCTAATTGCCACgg < 1:333711/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 2:159937/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 1:93238/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 1:759297/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 1:722531/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCCCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 2:651297/90‑1 (MQ=255)
cgcgTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACgg < 2:637669/90‑1 (MQ=255)
gcgTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGc > 1:777873/1‑90 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 1:791955/90‑1 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 1:585049/90‑1 (MQ=255)
ttCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATcc < 1:426168/90‑1 (MQ=255)
gTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACg < 1:778380/90‑1 (MQ=255)
tctcTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCACCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACgg < 1:548157/90‑1 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACgg < 2:196213/77‑1 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACgg > 1:196213/1‑77 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCt > 2:141247/1‑90 (MQ=255)
gttgttCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCt < 2:686437/90‑1 (MQ=255)
|
GTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCT > NZ_CP009273/4306605‑4306777
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGC > NZ_CP009273/4306603‑4306780
|
GCGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTC > SRR3722079.610208/1‑100 (MQ=60)
GTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGAT > SRR3722079.770724/1‑100 (MQ=60)
gaagacggcatacgagatcctctctggtctcgtgggctcggagatgtgtataagagccagCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCG < SRR3722079.711212/40‑1 (MQ=60)
GTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATC > SRR3722079.482169/1‑100 (MQ=60)
GATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCG > SRR3722079.841695/1‑100 (MQ=60)
GTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGCTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCA > SRR3722079.644237/1‑100 (MQ=60)
CGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGG < SRR3722079.76318/100‑1 (MQ=60)
GGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGC > SRR3722079.786209/1‑100 (MQ=60)
CGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCTAATTGCCACGGCATCCAGTAC < SRR3722079.336362/100‑1 (MQ=60)
CGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTAC < SRR3722079.93969/100‑1 (MQ=60)
CGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTAC < SRR3722079.767418/100‑1 (MQ=60)
CGCGTTTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTAC < SRR3722079.730252/100‑1 (MQ=60)
TTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGG < SRR3722079.590852/100‑1 (MQ=60)
TTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGG < SRR3722079.429847/100‑1 (MQ=60)
TTCTGCGTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGG < SRR3722079.800441/100‑1 (MQ=60)
GTCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGC < SRR3722079.786722/100‑1 (MQ=60)
TCTCTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCACCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCC < SRR3722079.553400/100‑1 (MQ=60)
CTTCGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCctg > SRR3722079.197904/1‑97 (MQ=60)
CGATGGCGTTGTTCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGGGGTGATGCCGCTCGC > SRR3722079.170507/1‑100 (MQ=60)
|
GCGTGGTGTGATGCGGCAGTTCGCAGCGCAGATGCAGACGGTGCTCGGCGCGGTTGACGCCGCGTTTCTGCGTCTCTTCGATGGCGTTGATCATCTTCTCCAGATTCTCCAGCCGATCGCCGCCGTCGCGCACGTCGCCAATTGCCACGGCATCCAGTACGGTGGTGATGCCGCTCGC > NZ_CP009273/4306603‑4306780
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
