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 |
1,174,665 |
T→G |
L206W (TTG→TGG) |
nagK → |
N‑acetylglucosamine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,174,665 | 0 | T | G | 94.1%
| 103.1
/ ‑0.8
| 34 | L206W (TTG→TGG) | nagK | N‑acetylglucosamine kinase |
| Reads supporting (aligned to +/- strand): ref base T (1/1); new base G (21/11); total (22/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.37e-01 |
GCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGC > NZ_CP009273/1174596‑1174749
|
gCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTg > 1:445067/1‑90 (MQ=255)
cTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTgc > 2:807471/1‑90 (MQ=255)
tGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTgcg < 2:985806/90‑1 (MQ=255)
gCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTgcgc > 2:80418/1‑90 (MQ=255)
gCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTgcgc > 2:530656/1‑90 (MQ=255)
aTTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCtt > 2:1357232/1‑90 (MQ=255)
gAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTAt > 1:37738/1‑90 (MQ=255)
aaaTTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATCATCATCAACCGTGGCAGGc > 1:1561363/1‑66 (MQ=255)
aaaTTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATCATCATCAACCGTGGCAGGc < 2:1561363/66‑1 (MQ=255)
ttATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCa > 1:1408058/1‑90 (MQ=255)
tgtctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCg > 1:1545041/1‑90 (MQ=255)
tgtctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCg > 2:206131/1‑90 (MQ=255)
gtctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGa < 1:807471/90‑1 (MQ=255)
ctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGc < 1:208067/55‑1 (MQ=255)
ctgGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGc > 2:208067/1‑55 (MQ=255)
ggTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATTAAGGCGATGAg > 2:1413892/1‑90 (MQ=255)
ggTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATTAAGGCGATGAg < 1:1413892/90‑1 (MQ=255)
ggTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAg < 2:1497222/90‑1 (MQ=255)
ggTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAg < 2:51910/90‑1 (MQ=255)
ggTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAg < 1:1544725/90‑1 (MQ=255)
gTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGc < 2:1485889/90‑1 (MQ=255)
gTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCaa < 2:200093/90‑1 (MQ=255)
tttGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAgg < 2:901907/90‑1 (MQ=255)
tGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGgc > 2:571522/1‑90 (MQ=255)
cacTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTAt > 1:28726/1‑90 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTg > 1:10178/1‑90 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTg > 1:1119190/1‑90 (MQ=255)
tattatCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTg > 1:744367/1‑90 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGgcg > 2:834972/1‑63 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGgcg < 1:834972/63‑1 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATttatta > 2:594244/1‑90 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATttatta > 1:1580097/1‑90 (MQ=255)
caACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATttatta > 1:895174/1‑90 (MQ=255)
aCCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGc > 2:619431/1‑90 (MQ=255)
|
GCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGC > NZ_CP009273/1174596‑1174749
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ 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
CTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTG > NZ_CP009273/1174582‑1174759
|
agcgtcagatgtgtataagagacagAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATT < SRR3722078.210583/75‑1 (MQ=60)
GGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTG > SRR3722078.450395/1‑100 (MQ=60)
TGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTAT > SRR3722078.38191/1‑100 (MQ=60)
GCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATCATCATCAACCGTGGCAGGCTCCCGAAATTctgtctcttataca > SRR3722078.1586773/1‑86 (MQ=60)
GCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCA > SRR3722078.1430900/1‑100 (MQ=60)
GAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCG > SRR3722078.1570218/1‑100 (MQ=60)
GTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCA < SRR3722078.818133/100‑1 (MQ=60)
GGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATTAAGGCGATGAGCAGGCAAGGG < SRR3722078.1436849/100‑1 (MQ=60)
GGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGG < SRR3722078.1569897/100‑1 (MQ=60)
atgtgtataagagacagCTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGC < SRR3722078.846080/83‑1 (MQ=60)
GGCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGActgtctcttatacacatctgacgctgccgacgatggcggtcgtgtagatctcggtgg > SRR3722078.1546275/1‑43 (MQ=60)
GCTGTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTAT > SRR3722078.29082/1‑100 (MQ=60)
GTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTG > SRR3722078.1136276/1‑100 (MQ=60)
GTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTG > SRR3722078.10290/1‑100 (MQ=60)
GTATCAACACTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTG > SRR3722078.753798/1‑100 (MQ=60)
CTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTA > SRR3722078.907205/1‑100 (MQ=60)
CTATTATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTA > SRR3722078.1605823/1‑100 (MQ=60)
ATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCtgtctcttatacacatctgacgctgccgacgat > SRR3722078.1178937/1‑67 (MQ=60)
ATCATCAACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCctgtctcttatacaca > SRR3722078.165117/1‑84 (MQ=60)
ACCGTGGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTG > SRR3722078.1188225/1‑100 (MQ=60)
|
CTGTGGTCAGCATGGCTGCATTGAAAATTATCTGTCTGGTCGCGGTTTTGCGTGGCTGTATCAACACTATTATCATCAACCGTTGCAGGCTCCCGAAATTATTGCGCTTTATGATCAAGGCGATGAGCAGGCAAGGGCGCACGTTGAGCGTTATCTGGATTTATTAGCGGTTTGTCTG > NZ_CP009273/1174582‑1174759
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
