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 |
601,986 |
A→G |
F285S (TTC→TCC) |
ybdK ← |
YbdK family carboxylate‑amine ligase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 601,986 | 0 | A | G | 97.7%
| 136.7
/ NA
| 43 | F285S (TTC→TCC) | ybdK | YbdK family carboxylate‑amine ligase |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (19/23); total (19/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAAT > NZ_CP009273/601900‑602071
|
aTCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAAc < 2:1423737/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGtt < 2:1509368/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGtt < 1:1266196/90‑1 (MQ=255)
cAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGtt < 1:164072/90‑1 (MQ=255)
tCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATAc > 1:410215/1‑90 (MQ=255)
ttAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATAcagca < 1:422238/90‑1 (MQ=255)
cGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa < 2:1044631/90‑1 (MQ=255)
cGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa < 2:104388/90‑1 (MQ=255)
tCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATc > 1:951211/1‑90 (MQ=255)
gacgaTCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa > 1:362970/1‑85 (MQ=255)
gacgaTCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa < 2:362970/85‑1 (MQ=255)
gacgaTCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCtt < 1:271247/90‑1 (MQ=255)
gacgaTCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCtt < 2:20193/90‑1 (MQ=255)
tcCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTg < 2:652622/90‑1 (MQ=255)
gtgtGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGa < 1:900305/87‑1 (MQ=255)
gtgtGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGa > 2:900305/1‑87 (MQ=255)
gtgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGttt > 2:1159105/1‑90 (MQ=255)
gtgCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGttt > 2:935930/1‑90 (MQ=255)
gCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTaa > 1:1530930/1‑90 (MQ=255)
cGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTaaa > 1:483447/1‑90 (MQ=255)
gATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACg > 2:1241866/1‑90 (MQ=255)
cGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCt < 2:342077/75‑1 (MQ=255)
cGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCt > 1:342077/1‑75 (MQ=255)
atgaCGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTcc < 1:1189722/90‑1 (MQ=255)
gaCGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGt > 2:781519/1‑90 (MQ=255)
gaCGCCTTCAAGCCCAAAGCCGCAGGGCCTGGAACGGGTTAAATTTTTAAACAAGTTATTTTTTTTCCTGATGTTTAACGGGGGTTTCCg < 1:39705/90‑1 (MQ=255)
aCGCCTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTc < 2:1417194/90‑1 (MQ=255)
ccTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGt > 1:1168733/1‑90 (MQ=255)
cTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa > 1:12626/1‑52 (MQ=255)
cTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTa < 2:12626/52‑1 (MQ=255)
cTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTa > 2:1340592/1‑90 (MQ=255)
cTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTa > 2:898111/1‑90 (MQ=255)
cTTCAAGCCCATAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTa > 2:39705/1‑90 (MQ=255)
aTAGCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGc > 1:491806/1‑90 (MQ=255)
gCGACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGt < 2:785896/90‑1 (MQ=255)
gACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAg > 2:1131576/1‑90 (MQ=255)
gACA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAg > 2:948351/1‑90 (MQ=255)
cA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc < 1:265299/90‑1 (MQ=255)
cA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc < 2:761619/90‑1 (MQ=255)
cA‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGcc < 2:1374667/90‑1 (MQ=255)
a‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCt < 2:703511/90‑1 (MQ=255)
a‑GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCt < 2:1271362/90‑1 (MQ=255)
cTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAAt < 1:935930/90‑1 (MQ=255)
|
ATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACA‑GGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAAT > NZ_CP009273/601900‑602071
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCGCC > NZ_CP009273/601888‑602081
|
TTTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGA < SRR3722078.396588/100‑1 (MQ=60)
TTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAA < SRR3722078.661207/100‑1 (MQ=60)
TTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAA < SRR3722078.1304483/100‑1 (MQ=60)
TTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAA < SRR3722078.1009922/100‑1 (MQ=60)
TCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCCCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGT < SRR3722078.1219473/100‑1 (MQ=60)
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAC > SRR3722078.415173/1‑100 (MQ=60)
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAC < SRR3722078.1286288/100‑1 (MQ=60)
CAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATAC < SRR3722078.165979/100‑1 (MQ=60)
CCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATC > SRR3722078.964572/1‑100 (MQ=60)
GTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTT > SRR3722078.367399/1‑100 (MQ=60)
TTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTT < SRR3722078.427329/100‑1 (MQ=60)
GACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATG < SRR3722078.274558/100‑1 (MQ=60)
TCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAA > SRR3722078.1555873/1‑100 (MQ=60)
CTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAA > SRR3722078.489184/1‑100 (MQ=60)
CCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACG < SRR3722078.912390/100‑1 (MQ=60)
GTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACtgtc > SRR3722078.346264/1‑96 (MQ=60)
GGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGT > SRR3722078.1186895/1‑100 (MQ=60)
GTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCctgtctcttatacacatctgacgctgcc > SRR3722078.12773/1‑72 (MQ=60)
ATGACGCCTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACC < SRR3722078.1208321/100‑1 (MQ=60)
CTTCAAGCCCATAGCGACAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGC > SRR3722078.497637/1‑100 (MQ=60)
CAGGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATC < SRR3722078.268542/100‑1 (MQ=60)
GGCCTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCC > SRR3722078.1057695/1‑100 (MQ=60)
CTGGGAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCGCC < SRR3722078.948889/100‑1 (MQ=60)
|
TTTTTTCCAGCAATCGCAAGGTATCTTCCGTTAGCGGTCGACGATCTCCAGTGTGCGGATCGGTGATGACGCCTTCAAGCCCATAGCGACAGGCCTGGAAACGGTTGAATTTATACAGCAGGTAATCTTTTTCCTGATGTTTAAACGGGCGTTCCGTCAGTAACCAGTGGGCGGTAGCCTGAATTAATCCCGCC > NZ_CP009273/601888‑602081
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
