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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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 | 97.8%
| 142.3
/ ‑3.7
| 45 | E522G (GAA→GGA) | yhiJ | YhiJ/YhiL family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (26/18); total (26/19) |
| Fisher's exact test for biased strand distribution p-value = 4.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCA > NZ_CP009273/3624299‑3624472
|
gTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa > 2:45958/1‑90 (MQ=255)
aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg < 2:352362/90‑1 (MQ=255)
ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg > 2:281487/1‑90 (MQ=255)
tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg < 2:315538/90‑1 (MQ=255)
tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg < 1:551089/90‑1 (MQ=255)
ttCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGAc < 2:39990/90‑1 (MQ=255)
tCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACt < 1:281487/90‑1 (MQ=255)
cATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACtt > 2:442937/1‑90 (MQ=255)
tgttgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAGGACTTcc < 2:536441/90‑1 (MQ=255)
cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg > 2:185201/1‑90 (MQ=255)
ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGt < 1:495229/90‑1 (MQ=255)
ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 1:185201/90‑1 (MQ=255)
cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc > 1:168037/1‑90 (MQ=255)
cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc > 1:506876/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 1:465087/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGACCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 2:527423/1‑90 (MQ=255)
gCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAg > 2:220687/1‑90 (MQ=255)
tGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGc > 2:38901/1‑90 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg > 1:198253/1‑75 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg < 2:198253/75‑1 (MQ=255)
aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 2:365401/74‑1 (MQ=255)
aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt > 1:365401/1‑74 (MQ=255)
aTTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCa > 2:451101/1‑90 (MQ=255)
ttGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc > 2:562878/1‑90 (MQ=255)
ttGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc > 2:447274/1‑90 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCa < 1:470638/46‑1 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCa > 1:115663/1‑63 (MQ=255)
tgtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCa < 2:115663/63‑1 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa > 2:194281/1‑90 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa > 1:465560/1‑90 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCa < 1:227452/90‑1 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc < 2:142810/81‑1 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc > 1:142810/1‑81 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg > 1:556054/1‑90 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg > 1:344492/1‑90 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg > 2:562415/1‑90 (MQ=255)
ttCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTaa > 2:315453/1‑90 (MQ=255)
gCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc > 2:171046/1‑64 (MQ=255)
gCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc < 1:171046/64‑1 (MQ=255)
aTAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgc < 1:185880/90‑1 (MQ=255)
cATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGa > 1:347771/1‑90 (MQ=255)
tttCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAAc < 2:168037/90‑1 (MQ=255)
tCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAt < 1:315453/90‑1 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGc > 1:558311/1‑68 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGc < 2:558311/68‑1 (MQ=255)
tttcCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCa < 2:301378/90‑1 (MQ=255)
tttcCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCa < 1:442937/90‑1 (MQ=255)
|
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCA > NZ_CP009273/3624299‑3624472
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACT > NZ_CP009273/3624299‑3624483
|
gtcgtcggcagcgtcagatgtgtataagagacagGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAG < SRR3722092.479976/66‑1 (MQ=60)
TATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGG < SRR3722092.562150/100‑1 (MQ=60)
TCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGT < SRR3722092.286321/100‑1 (MQ=60)
GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC > SRR3722092.170853/1‑100 (MQ=60)
GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC > SRR3722092.517018/1‑100 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC > SRR3722092.474293/1‑100 (MQ=60)
GGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGC < SRR3722092.505091/100‑1 (MQ=60)
GGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGC < SRR3722092.188282/100‑1 (MQ=60)
GTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCctgtc > SRR3722092.201529/1‑95 (MQ=60)
GAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCtgtct > SRR3722092.372224/1‑95 (MQ=60)
GCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTctgtctcttatacacat > SRR3722092.117629/1‑83 (MQ=60)
CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGTTTATCTCATTCCCTGCACCA > SRR3722092.157104/1‑100 (MQ=60)
CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCA > SRR3722092.474777/1‑100 (MQ=60)
GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG > SRR3722092.145204/1‑100 (MQ=60)
GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG > SRR3722092.567213/1‑100 (MQ=60)
GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG > SRR3722092.350678/1‑100 (MQ=60)
tgtgtataagagacagCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGG < SRR3722092.173909/84‑1 (MQ=60)
GTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTT < SRR3722092.231179/100‑1 (MQ=60)
GGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGA > SRR3722092.354049/1‑100 (MQ=60)
ATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACA < SRR3722092.188968/100‑1 (MQ=60)
GTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATctgtctcttata > SRR3722092.569515/1‑88 (MQ=60)
TCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCA < SRR3722092.321034/100‑1 (MQ=60)
TTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTAC < SRR3722092.451637/100‑1 (MQ=60)
TTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACT < SRR3722092.197506/100‑1 (MQ=60)
|
GTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTACT > NZ_CP009273/3624299‑3624483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
