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 |
4,336,254 |
T→G |
D297A (GAC→GCC) |
fumB ← |
class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,336,254 | 0 | T | G | 95.5%
| 72.3
/ ‑3.3
| 22 | D297A (GAC→GCC) | fumB | class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base G (13/8); total (13/9) |
| Fisher's exact test for biased strand distribution p-value = 4.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.78e-01 |
CGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATC > NZ_CP009273/4336166‑4336339
|
cGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTc < 2:239203/90‑1 (MQ=255)
gCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCg > 1:163593/1‑90 (MQ=255)
aTGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGcgcg < 1:466637/90‑1 (MQ=255)
tGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGa < 2:161692/90‑1 (MQ=255)
aCGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTa > 2:647220/1‑90 (MQ=255)
aCGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTa > 1:452551/1‑90 (MQ=255)
aCGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTa > 2:462313/1‑90 (MQ=255)
gTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTAttt < 1:305233/90‑1 (MQ=255)
gTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTAttt < 1:647220/90‑1 (MQ=255)
cAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGGTAACGCGAATGGCGTGCGCGAAGTATTTAc > 2:30354/1‑90 (MQ=255)
gCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCg > 1:80234/1‑90 (MQ=255)
gCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCaaa > 1:18272/1‑90 (MQ=255)
gACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg > 1:429923/1‑90 (MQ=255)
ggATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTCTTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGc < 1:760784/90‑1 (MQ=255)
aTGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCct > 1:347617/1‑90 (MQ=255)
cgcCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCtt < 1:122242/90‑1 (MQ=255)
tGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCcagc > 2:188340/1‑90 (MQ=255)
gACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGtt < 1:9013/90‑1 (MQ=255)
gATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAg > 1:73554/1‑90 (MQ=255)
gAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCca > 1:569691/1‑66 (MQ=255)
gAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCca < 2:569691/66‑1 (MQ=255)
aaTGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATc > 2:693185/1‑90 (MQ=255)
|
CGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATC > NZ_CP009273/4336166‑4336339
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
CGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > NZ_CP009273/4336155‑4336345
|
CGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGG < SRR3722072.229532/100‑1 (MQ=60)
CGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGG > SRR3722072.357021/1‑100 (MQ=60)
GTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCG > SRR3722072.166438/1‑100 (MQ=60)
TGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTG < SRR3722072.155110/100‑1 (MQ=60)
CTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTA > SRR3722072.460833/1‑100 (MQ=60)
ATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTAC < SRR3722072.475160/100‑1 (MQ=60)
GTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCG > SRR3722072.81727/1‑100 (MQ=60)
GGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAA > SRR3722072.18614/1‑100 (MQ=60)
GTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAAC < SRR3722072.310522/100‑1 (MQ=60)
GTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAAC < SRR3722072.658774/100‑1 (MQ=60)
CGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAG > SRR3722072.437750/1‑100 (MQ=60)
ACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCT > SRR3722072.353736/1‑100 (MQ=60)
GGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTCTTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGC < SRR3722072.774192/100‑1 (MQ=60)
CGCCGTGACGTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTC < SRR3722072.124468/100‑1 (MQ=60)
GTGGCAGACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAG > SRR3722072.74924/1‑100 (MQ=60)
GACGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGAC < SRR3722072.9187/100‑1 (MQ=60)
CGGATAACGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGctgtctcttataca > SRR3722072.579875/1‑86 (MQ=60)
CGCGAATGGCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > SRR3722072.413926/1‑100 (MQ=60)
|
CGGTTGATTTTCGCTTTAATGTTACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGTTTCTGGGCCTCTTCCAGCAGTTCCTGTTCCAGCTGGACATCGCGGAA > NZ_CP009273/4336155‑4336345
|
| 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: ‑ |
