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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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 | 100.0%
| 131.1
/ NA
| 39 | E522G (GAA→GGA) | yhiJ | YhiJ/YhiL family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/15); total (24/15) |
AACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCA > NZ_CP009273/3624301‑3624472
|
aaCATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATg > 2:221161/1‑90 (MQ=255)
cATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCt > 1:210520/1‑90 (MQ=255)
ttAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTgg > 2:486816/1‑90 (MQ=255)
aaTATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa < 1:71479/90‑1 (MQ=255)
aaTATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTa > 1:486985/1‑90 (MQ=255)
tatTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAg < 2:286076/90‑1 (MQ=255)
ttCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGAc < 1:498729/90‑1 (MQ=255)
tgtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAgg > 1:404491/1‑90 (MQ=255)
gtCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAggg < 1:375724/90‑1 (MQ=255)
cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg > 1:91733/1‑90 (MQ=255)
cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg > 2:244415/1‑90 (MQ=255)
cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg < 2:210520/90‑1 (MQ=255)
cTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAg < 1:244415/90‑1 (MQ=255)
ggTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 2:486985/90‑1 (MQ=255)
cAGATCTGTAACATTGTGCGCCTTCTGATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGGCTTCCAGGGAGTGGTTAtc > 1:515550/1‑90 (MQ=255)
cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc > 1:465036/1‑90 (MQ=255)
cAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtc > 1:211288/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 1:463214/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTAtctc > 1:442200/1‑90 (MQ=255)
gagCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGCGGTTAtctc > 2:463523/1‑90 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt < 2:7620/79‑1 (MQ=255)
gTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGt > 1:7620/1‑79 (MQ=255)
tAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc < 2:346534/90‑1 (MQ=255)
ttGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc < 2:166587/90‑1 (MQ=255)
ttGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAc < 2:339336/90‑1 (MQ=255)
gtgCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCACGCCCTGCACCa > 1:144884/1‑90 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg > 1:47627/1‑90 (MQ=255)
gcgcCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAgg > 1:443878/1‑90 (MQ=255)
ttCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc > 2:463147/1‑76 (MQ=255)
ttCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGccc < 1:463147/76‑1 (MQ=255)
ttCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTaa > 2:250413/1‑90 (MQ=255)
tCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAAt > 2:406801/1‑90 (MQ=255)
aaaGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCaa > 2:509248/1‑90 (MQ=255)
aGGCATAAGTCCATTTCTATTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAAtt > 2:476648/1‑90 (MQ=255)
tAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTatgca < 2:442200/90‑1 (MQ=255)
tCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAt < 2:352975/90‑1 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc > 2:383514/1‑54 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCAcc < 1:383514/54‑1 (MQ=255)
gTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACAttct > 2:413954/1‑90 (MQ=255)
tttcCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCGGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCa < 1:4844/90‑1 (MQ=255)
tttcCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCa < 1:250413/90‑1 (MQ=255)
|
AACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCA > NZ_CP009273/3624301‑3624472
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTAC > NZ_CP009273/3624293‑3624482
|
CAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCT > SRR3722114.212559/1‑100 (MQ=60)
TAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTA > SRR3722114.493083/1‑100 (MQ=60)
AATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAG < SRR3722114.72211/100‑1 (MQ=60)
ATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGG > SRR3722114.409419/1‑100 (MQ=60)
TTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAG > SRR3722114.92699/1‑100 (MQ=60)
TTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAG < SRR3722114.504985/100‑1 (MQ=60)
GTCTATGGTTCAGATCTGTAACATTGTGCGCCTTCTGATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGGCTTCCAGGGAGTGGTTATC > SRR3722114.522011/1‑100 (MQ=60)
GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC < SRR3722114.380241/100‑1 (MQ=60)
GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC > SRR3722114.470842/1‑100 (MQ=60)
GTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATC > SRR3722114.213334/1‑100 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC > SRR3722114.447669/1‑100 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC > SRR3722114.468999/1‑100 (MQ=60)
CTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTC < SRR3722114.246782/100‑1 (MQ=60)
GTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCC > SRR3722114.7697/1‑100 (MQ=60)
CTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCACGCCCTGCACCA > SRR3722114.146367/1‑100 (MQ=60)
GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG > SRR3722114.449376/1‑100 (MQ=60)
GTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGG > SRR3722114.48093/1‑100 (MQ=60)
acagATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGG < SRR3722114.468931/96‑1 (MQ=60)
ggctcggagatgtgtataagagacagGTCCATTTCTGTTTTTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATT < SRR3722114.388144/74‑1 (MQ=60)
TTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCGGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTAC < SRR3722114.4894/100‑1 (MQ=60)
TTTCCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTAC < SRR3722114.252880/100‑1 (MQ=60)
|
CAGATAGTAACATTAATATTCATGTTGTCTATGGTTCAGAGCTGTAACATTGTGCGCCTTCTAATCAAAGGCATAAGTCCATTTCTGTTTTTTTCATGCTGGTAAGACTTCCAGGGAGTGGTTATCTCAGGCCCTGCACCAGGGTTAATTTGGCAATTATGCATGCTGAACATTCTTCCAGCATGTTTAC > NZ_CP009273/3624293‑3624482
|
| 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: ‑ |
