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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,202,171 |
G→C |
W242C (TGG→TGC) |
yehP → |
VWA domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,202,171 | 0 | G | C | 94.7%
| 56.6
/ ‑3.0
| 19 | W242C (TGG→TGC) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base C (7/11); total (7/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.10e-01 |
ACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAT > NZ_CP009273/2202093‑2202246
|
aCTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCgg < 2:402132/90‑1 (MQ=255)
aCTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCgg > 2:612183/1‑90 (MQ=255)
cTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc < 2:28582/90‑1 (MQ=255)
ttGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATc > 2:667921/1‑90 (MQ=255)
gATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCtg > 1:652769/1‑90 (MQ=255)
tCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCtggt > 1:442783/1‑90 (MQ=255)
aGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCg > 2:259373/1‑90 (MQ=255)
ggATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGttt < 1:633845/90‑1 (MQ=255)
gATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTg < 1:244505/90‑1 (MQ=255)
ggTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAg < 2:680971/90‑1 (MQ=255)
gATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGcgtc < 1:556994/90‑1 (MQ=255)
gATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAtct < 2:442783/90‑1 (MQ=255)
aCTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACgg < 1:299875/90‑1 (MQ=255)
ctctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGc > 2:715310/1‑90 (MQ=255)
ctctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGc > 2:718166/1‑90 (MQ=255)
gCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGAc < 2:459196/90‑1 (MQ=255)
aTGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGcc < 1:309159/90‑1 (MQ=255)
aTGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGcc < 2:440863/90‑1 (MQ=255)
gcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAt < 2:656447/90‑1 (MQ=255)
|
ACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAT > NZ_CP009273/2202093‑2202246
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ 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
CTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > NZ_CP009273/2202099‑2202263
|
CTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTG > SRR3722112.662951/1‑100 (MQ=60)
TACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGT > SRR3722112.448919/1‑100 (MQ=60)
GGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCG < SRR3722112.643667/100‑1 (MQ=60)
GATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGT < SRR3722112.247405/100‑1 (MQ=60)
GATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCA < SRR3722112.565434/100‑1 (MQ=60)
ACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCACACGTTGC < SRR3722112.303331/100‑1 (MQ=60)
ATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAG < SRR3722112.312705/100‑1 (MQ=60)
GTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > SRR3722112.528112/1‑100 (MQ=60)
|
CTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > NZ_CP009273/2202099‑2202263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
