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 |
2,122,248 |
C→A |
R41L (CGC→CTC) |
wcaF ← |
colanic acid biosynthesis acetyltransferase WcaF |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,122,248 | 0 | C | A | 93.3%
| 42.6
/ ‑2.6
| 15 | R41L (CGC→CTC) | wcaF | colanic acid biosynthesis acetyltransferase WcaF |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (3/11); total (4/11) |
| Fisher's exact test for biased strand distribution p-value = 2.67e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.00e-01 |
GGTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCC > NZ_CP009273/2122169‑2122328
|
ggTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATAc > 2:689878/1‑90 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGAcc < 2:774041/90‑1 (MQ=255)
cTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCAAcc < 2:405523/90‑1 (MQ=255)
acggacgAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAgg > 1:18213/1‑90 (MQ=255)
tAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATAttg < 1:371686/90‑1 (MQ=255)
tCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGc < 1:853890/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATCCTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGccc < 1:281143/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGccc < 1:494908/90‑1 (MQ=255)
cTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGccc < 1:63356/90‑1 (MQ=255)
tATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCcca > 2:477215/1‑90 (MQ=255)
tttttGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCccacc < 1:115048/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 1:467953/90‑1 (MQ=255)
ccGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGc < 2:469439/90‑1 (MQ=255)
aaaaGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTgcc < 1:905492/90‑1 (MQ=255)
gCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGccc > 1:836103/1‑90 (MQ=255)
|
GGTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCC > NZ_CP009273/2122169‑2122328
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 30 ≤ 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
TAATTTCCACGGATAGGTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCG > NZ_CP009273/2122154‑2122347
|
TAATTTCCACGGATAGGTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATAC < SRR3722072.312318/100‑1 (MQ=60)
ATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGG > SRR3722072.18552/1‑100 (MQ=60)
TAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTAC < SRR3722072.378293/100‑1 (MQ=60)
TCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAAT < SRR3722072.868635/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATCCTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722072.285949/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722072.503851/100‑1 (MQ=60)
CTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTG < SRR3722072.64519/100‑1 (MQ=60)
TTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCAC < SRR3722072.117161/100‑1 (MQ=60)
CCGAATAAACGTAATAAAAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAG < SRR3722072.476492/100‑1 (MQ=60)
TAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCC > SRR3722072.850588/1‑100 (MQ=60)
AAAAGCCCGCCAGAGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAAC < SRR3722072.921073/100‑1 (MQ=60)
AGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCG > SRR3722072.265691/1‑100 (MQ=60)
|
TAATTTCCACGGATAGGTAATTTTTACTGACGGACGAATAACTACGTTTTTTCCTATTTTTGCTCCGAATAAACGTAATAAAAAAGCCCGCCAGCGATACAATACTTGTGGCGACCAGGCAAATATTGTTGCCTGTACTGCCCACCATAATTGCACTTTAATAGCGTTGCCGCCCCGGAACCCTTTCGGCACCG > NZ_CP009273/2122154‑2122347
|
| 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: ‑ |
