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 |
2,778,934 |
(T)6→5 |
intergenic (‑564/+187) |
BW25113_RS25705 ← / ← BW25113_RS13825 |
DUF5507 domain‑containing protein/tRNA‑Ile |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,778,929 | 0 | T | . | 97.1%
| 135.9
/ ‑0.8
| 36 | intergenic (‑559/+192) | BW25113_RS25705/BW25113_RS13825 | DUF5507 domain‑containing protein/tRNA‑Ile |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base . (18/16); total (19/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.85e-01 |
AAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTC > NZ_CP009273/2778840‑2779012
|
aaGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAt < 1:660579/90‑1 (MQ=255)
gTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCAtttttc < 1:679764/90‑2 (MQ=255)
aaaTGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTAc > 1:135040/1‑90 (MQ=255)
aTGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACtt > 2:73451/1‑90 (MQ=255)
aTGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACtt > 2:102808/1‑90 (MQ=255)
aataCTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGaa < 1:231246/90‑1 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 1:31365/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 1:321716/1‑90 (MQ=255)
ctGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTa > 2:256035/1‑90 (MQ=255)
ggCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACt > 2:275867/1‑90 (MQ=255)
gCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTg < 2:292872/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:526269/90‑1 (MQ=255)
tttATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGAt < 2:618503/90‑1 (MQ=255)
tATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATgg > 2:669336/1‑90 (MQ=255)
tAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAAt > 1:73730/1‑90 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATATCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 2:635413/90‑1 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 2:569639/90‑1 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 1:73451/90‑1 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 2:321716/90‑1 (MQ=255)
aTTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 1:102808/90‑1 (MQ=255)
ttAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGTATAAATACATTGc < 1:78461/90‑1 (MQ=255)
ccACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGc > 1:511984/1‑90 (MQ=255)
ccACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGc > 1:403340/1‑90 (MQ=255)
cacaTGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCg < 2:157699/90‑1 (MQ=255)
acaTGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGaa < 1:469393/56‑1 (MQ=255)
acaTGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGaa > 2:469393/1‑56 (MQ=255)
tAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCg < 1:310515/84‑1 (MQ=255)
tAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCg > 2:310515/1‑84 (MQ=255)
tAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCAc < 1:271265/90‑1 (MQ=255)
tAAGCAATTTGCCCGCTTGGCANAGAAGG‑AATTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCAc < 2:232521/90‑1 (MQ=255)
aaGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACg > 1:282336/1‑90 (MQ=255)
aGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGt < 1:467194/90‑1 (MQ=255)
gCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACAcc > 1:175055/1‑90 (MQ=255)
gCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc < 2:529184/58‑1 (MQ=255)
gCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATAc > 1:529184/1‑58 (MQ=255)
gCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCa > 1:340434/1‑90 (MQ=255)
gCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTc > 2:427383/1‑90 (MQ=255)
gCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTc > 1:524106/1‑90 (MQ=255)
|
AAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTC > NZ_CP009273/2778840‑2779012
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTC > NZ_CP009273/2778840‑2779012
|
AAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGT < SRR3722112.670888/100‑1 (MQ=60)
GGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTAC > SRR3722112.136725/1‑100 (MQ=60)
GTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTT < SRR3722112.690394/100‑1 (MQ=60)
TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTA > SRR3722112.31765/1‑100 (MQ=60)
TGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTA > SRR3722112.325498/1‑100 (MQ=60)
gcgtcagatgtgtataagagacagACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGA < SRR3722112.476078/76‑1 (MQ=60)
AATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGA < SRR3722112.234021/100‑1 (MQ=60)
GCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAAT > SRR3722112.74629/1‑100 (MQ=60)
ATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGG < SRR3722112.74345/100‑1 (MQ=60)
ATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGG < SRR3722112.104085/100‑1 (MQ=60)
TTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGC > SRR3722112.408665/1‑100 (MQ=60)
TTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGC > SRR3722112.519477/1‑100 (MQ=60)
TTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGTATAAATACATTGCAGTGGCGTGC < SRR3722112.79412/100‑1 (MQ=60)
TTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACG > SRR3722112.285612/1‑100 (MQ=60)
CACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTAC < SRR3722112.314076/100‑1 (MQ=60)
TAAGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAAC < SRR3722112.274435/100‑1 (MQ=60)
AGCAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACAC < SRR3722112.473846/100‑1 (MQ=60)
CAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACC > SRR3722112.177198/1‑100 (MQ=60)
CAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCtgtctcttatacacatctgac > SRR3722112.537018/1‑79 (MQ=60)
CAATTTGCCCGCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCA > SRR3722112.344633/1‑100 (MQ=60)
GCTTGGCATAGCAGGCA‑TTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTC > SRR3722112.531838/1‑100 (MQ=60)
|
AAGGGGTATAATAAATGATAATACTCTGGCTTTATCGTTAATTACTTAATTCCACATGTAAGCAATTTGCCCGCTTGGCATAGCAGGCATTTTTTCCAGGTACTTTTGAATGAGTACTGATGGATAAATACATTGCAGTGGCGTGCCACGTACCAAAACACCAGCCCTCATTC > NZ_CP009273/2778840‑2779012
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
