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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | 97.1%
| 100.7
/ ‑3.6
| 36 | W242C (TGG→TGC) | yehP | VWA domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); major base C (21/13); minor base T (0/1); total (22/14) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.45e-01 |
CAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGT > NZ_CP009273/2202085‑2202256
|
cAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAg > 2:1190984/1‑90 (MQ=255)
aTGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGtt > 2:253878/1‑90 (MQ=255)
cAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTAccc < 1:706251/90‑1 (MQ=255)
aaCTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCg < 2:1005023/90‑1 (MQ=255)
aaCTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCg < 1:78667/90‑1 (MQ=255)
gTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCAtt < 1:801122/90‑1 (MQ=255)
cTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAcc < 2:730716/90‑1 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 2:1047201/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 2:807815/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCAt > 2:547954/1‑90 (MQ=255)
gTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGGGATGGCGGCCTGTTTGGGCCAGTTACCCGGCATTCGTACCCAt > 1:716330/1‑90 (MQ=255)
tCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCtggt > 2:1475427/1‑90 (MQ=255)
aGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCg > 1:265414/1‑90 (MQ=255)
gATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTg > 1:1554827/1‑90 (MQ=255)
aTGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGAcaca > 1:1364101/1‑90 (MQ=255)
cGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTg < 2:1293337/90‑1 (MQ=255)
tGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGAtc < 2:1158953/90‑1 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGtt < 1:1577912/36‑1 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGtt > 2:1577912/1‑36 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCAc > 2:499045/1‑90 (MQ=255)
ccACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCAc > 2:1518345/1‑90 (MQ=255)
ctctGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGc > 2:1192291/1‑90 (MQ=255)
gATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGc > 1:603618/1‑90 (MQ=255)
gATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGc > 1:39362/1‑90 (MQ=255)
gATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGc > 2:1548914/1‑90 (MQ=255)
aTGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGcc > 1:665298/1‑90 (MQ=255)
ggcggcCTGTTTGTGCCAGTTACCCGGCCTTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGa < 1:686229/90‑1 (MQ=255)
ggcggcCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGa > 2:1136250/1‑90 (MQ=255)
gcggcCTGTTTGTGTCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGAt < 2:62542/90‑1 (MQ=255)
cggcCTGTTTGTGGCAGTTACCCGGCATTCCTAACCCTCTGGGGGCGTTTTACACAAGCGGCGGTTATTTCACGGGCGAAGTTGCCGATc > 1:735508/1‑90 (MQ=255)
ccTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCgg > 1:565487/1‑90 (MQ=255)
tGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTa < 1:1136250/90‑1 (MQ=255)
tGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTa > 2:772812/1‑90 (MQ=255)
gTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTag < 1:547954/90‑1 (MQ=255)
gTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTag < 1:816480/90‑1 (MQ=255)
tgtgCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGt < 2:472003/90‑1 (MQ=255)
|
CAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGT > NZ_CP009273/2202085‑2202256
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ 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
ACGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > NZ_CP009273/2202072‑2202263
|
gccatcgtcggcagcgtcagatgtgtataagagacagGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGC < SRR3722078.394550/63‑1 (MQ=60)
CGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCC < SRR3722078.1017946/100‑1 (MQ=60)
CGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCC < SRR3722078.1251278/100‑1 (MQ=60)
CGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCC < SRR3722078.291027/100‑1 (MQ=60)
caactccgccatcgtcggcagcgtcagatgtgtataagagacaGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTTCCCGGCATT < SRR3722078.1603596/57‑1 (MQ=60)
CAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTA < SRR3722078.714800/100‑1 (MQ=60)
agatctacactaccgccatcgtcggcagcgtcagatgtgtataagagacagACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAC < SRR3722078.1062826/49‑1 (MQ=60)
AACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTAC < SRR3722078.79595/100‑1 (MQ=60)
GGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGGGATGGCGGCCTGTTTGGGCCAGTTACCCGGCATTCGTACCCAT > SRR3722078.725154/1‑100 (MQ=60)
GTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATC < SRR3722078.811667/100‑1 (MQ=60)
GGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCG > SRR3722078.268657/1‑100 (MQ=60)
GATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTG > SRR3722078.1580142/1‑100 (MQ=60)
AAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACA > SRR3722078.1386045/1‑100 (MQ=60)
ACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGC > SRR3722078.39832/1‑100 (MQ=60)
ACTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGC > SRR3722078.610594/1‑100 (MQ=60)
CTCTGCGGTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCC > SRR3722078.672917/1‑100 (MQ=60)
GCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCCTAACCCTCTGGGGGCGTTTTACACAAGCGgcggttatttcacgggcgaagttgccgatc > SRR3722078.744747/1‑70 (MQ=58)
GTGATGGCGGCCTGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGG > SRR3722078.572115/1‑100 (MQ=60)
GGCGGCCTGTTTGTGCCAGTTACCCGGCCTTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAG < SRR3722078.694303/100‑1 (MQ=60)
TGTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAA < SRR3722078.1153675/100‑1 (MQ=60)
GTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCctgtctcttatacacatctgacgctgccgacgatggc > SRR3722078.183522/1‑63 (MQ=60)
GTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT < SRR3722078.554424/100‑1 (MQ=60)
GTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > SRR3722078.1094584/1‑100 (MQ=60)
GTTTGTGCCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT < SRR3722078.827280/100‑1 (MQ=60)
|
ACGCCAAAGCGAACAATGGCAACTGGTCTTACTGGTTGATCAAAGCGGATCGATGGTCGATTCGGTGATCCACTCTGCGGTGATGGCGGCCTGTTTGTGGCAGTTACCCGGCATTCGTACCCATCTGGTGGCGTTTGACACAAGCGTCGTTGATCTCACGGCAGACGTTGCCGATCCGGTAGAGTTATTAAT > NZ_CP009273/2202072‑2202263
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
