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 I209 R1
|
216 |
14.4 |
815930 |
96.1% |
784108 |
85.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,624,386 |
T→C |
E522G (GAA→GGA) |
yhiJ ← |
YhiJ/YhiL family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,624,386 | 0 | T | C | 100.0%
| 99.9
/ NA
| 31 | E522G (GAA→GGA) | yhiJ | YhiJ/YhiL family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/14); total (17/14) |
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT > NZ_CP009273/3624299‑3624468
|
gTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa > 2:78862/1‑90 (MQ=255)
tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg > 1:117116/1‑90 (MQ=255)
cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt > 2:114131/1‑90 (MQ=255)
tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa < 1:238395/79‑1 (MQ=255)
tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa > 2:238395/1‑79 (MQ=255)
tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg > 2:161720/1‑90 (MQ=255)
tCTATGGTTCAGAGCTGAAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGa < 2:324879/90‑1 (MQ=255)
tGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTgg > 2:45205/1‑90 (MQ=255)
ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 1:161720/90‑1 (MQ=255)
ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 1:358326/90‑1 (MQ=255)
gTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGtt < 2:25270/90‑1 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 1:300758/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 1:327799/1‑90 (MQ=255)
agCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCa < 2:385428/90‑1 (MQ=255)
gCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAg < 1:156016/90‑1 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg > 1:193493/1‑55 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg < 2:193493/55‑1 (MQ=255)
aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCa > 2:103425/1‑90 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc < 1:114131/90‑1 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc < 1:77582/89‑1 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc > 2:77582/1‑89 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg > 2:106888/1‑67 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg < 1:106888/67‑1 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc > 2:213637/1‑89 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc < 1:213637/89‑1 (MQ=255)
aaaGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCaa > 1:209460/1‑90 (MQ=255)
cATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatg < 2:791/90‑1 (MQ=255)
gTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgcatgc < 1:312052/90‑1 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct > 2:127444/1‑90 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct > 2:282690/1‑90 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct > 1:132392/1‑90 (MQ=255)
|
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT > NZ_CP009273/3624299‑3624468
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
CCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACTG > NZ_CP009273/3624292‑3624484
|
CCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGC < SRR3722091.199217/100‑1 (MQ=60)
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAG > SRR3722091.118890/1‑100 (MQ=60)
GATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAG < SRR3722091.242066/100‑1 (MQ=60)
gtataagagacAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC < SRR3722091.108522/89‑1 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC > SRR3722091.333482/1‑100 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC > SRR3722091.305868/1‑100 (MQ=60)
GGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGC < SRR3722091.164074/100‑1 (MQ=60)
GGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGC < SRR3722091.364614/100‑1 (MQ=60)
GTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACctgtctcttatacacatctgacgct > SRR3722091.196376/1‑75 (MQ=60)
GCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACC < SRR3722091.158299/100‑1 (MQ=60)
TTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAAT < SRR3722091.78787/100‑1 (MQ=60)
TGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATT < SRR3722091.115864/100‑1 (MQ=60)
TGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATT < SRR3722091.216918/100‑1 (MQ=60)
NCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAA > SRR3722091.212668/1‑100 (MQ=60)
GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT < SRR3722091.317400/100‑1 (MQ=60)
GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCT > SRR3722091.134380/1‑100 (MQ=60)
TCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACTG < SRR3722091.274638/100‑1 (MQ=60)
|
CCAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACTG > NZ_CP009273/3624292‑3624484
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
