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 |
1,331,016 |
A→G |
Y310C (TAT→TGT) |
acnA → |
aconitate hydratase AcnA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,331,016 | 0 | A | G | 100.0%
| 100.9
/ NA
| 31 | Y310C (TAT→TGT) | acnA | aconitate hydratase AcnA |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/18); total (13/18) |
TGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGT > NZ_CP009273/1330929‑1331097
|
tggGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAAtgtg > 1:212248/1‑90 (MQ=255)
aaaTTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGcc < 1:689004/90‑1 (MQ=255)
cgtctAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCtg < 2:636951/90‑1 (MQ=255)
cgtcgAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCtg < 2:1568180/90‑1 (MQ=255)
gtcgAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCtgt < 2:526717/90‑1 (MQ=255)
aaTTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGct < 2:223048/90‑1 (MQ=255)
tGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGa < 2:58414/90‑1 (MQ=255)
ggTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGAt < 1:1173551/90‑1 (MQ=255)
ggTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGAt > 1:1331828/1‑90 (MQ=255)
ggATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGt > 1:1040400/1‑90 (MQ=255)
ggATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGt > 2:786007/1‑90 (MQ=255)
gATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTa < 2:1331828/90‑1 (MQ=255)
tCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAAcc < 1:15731/90‑1 (MQ=255)
cACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAAccc > 1:1502414/1‑90 (MQ=255)
aCTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCt < 1:1096059/90‑1 (MQ=255)
aCTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCt > 2:1030593/1‑90 (MQ=255)
aCTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCt > 1:714925/1‑90 (MQ=255)
cGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGAtt < 1:90361/90‑1 (MQ=255)
gTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTa > 1:1143546/1‑90 (MQ=255)
tGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACa < 1:1211316/90‑1 (MQ=255)
ggCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATgtggtg > 2:912546/1‑44 (MQ=255)
ggCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATgtggtg < 1:912546/44‑1 (MQ=255)
ggCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACAt < 1:737311/90‑1 (MQ=255)
ggCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACAt < 2:1056370/90‑1 (MQ=255)
gCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATg > 1:1176156/1‑90 (MQ=255)
ccaTTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGgc < 1:786007/90‑1 (MQ=255)
aTTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGgcgc < 2:1176156/90‑1 (MQ=255)
ccAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCg < 1:531258/90‑1 (MQ=255)
cAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGa < 1:1066328/90‑1 (MQ=255)
atatGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAg > 2:43818/1‑90 (MQ=255)
atatGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAg > 1:890276/1‑90 (MQ=255)
gTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCa > 2:1500832/1‑90 (MQ=255)
cGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAgg > 2:145067/1‑90 (MQ=255)
gCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGt > 1:1434353/1‑90 (MQ=255)
|
TGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGT > NZ_CP009273/1330929‑1331097
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ 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
CATGGCGTGGTGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGTCGAGTTGGTCGAAAAA > NZ_CP009273/1330919‑1331113
|
CATGGCGTGGTGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTG > SRR3722078.214816/1‑100 (MQ=60)
TGGCGTGGTGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGT < SRR3722078.959383/100‑1 (MQ=60)
ccatcgtcggcagcgtcagatgtgtataagagacagCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGG < SRR3722078.924897/64‑1 (MQ=60)
AAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCT < SRR3722078.697148/100‑1 (MQ=60)
TTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGAT > SRR3722078.1353154/1‑100 (MQ=60)
GTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGT > SRR3722078.1055917/1‑100 (MQ=60)
GGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCC < SRR3722078.1191829/100‑1 (MQ=60)
GGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCC > SRR3722078.1526917/1‑100 (MQ=60)
GTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCT > SRR3722078.723711/1‑100 (MQ=60)
ATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTA > SRR3722078.1161145/1‑100 (MQ=60)
TCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACA < SRR3722078.15926/100‑1 (MQ=60)
ACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATG > SRR3722078.1194492/1‑100 (MQ=60)
ACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATG < SRR3722078.1112726/100‑1 (MQ=60)
CGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTT < SRR3722078.91423/100‑1 (MQ=60)
TGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAG < SRR3722078.1230358/100‑1 (MQ=60)
GGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGC < SRR3722078.746593/100‑1 (MQ=60)
cggcagcgtcagatgtgtataagagacagGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCG < SRR3722078.1055239/71‑1 (MQ=60)
ACCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAG > SRR3722078.902248/1‑100 (MQ=60)
CCATTGCCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGA < SRR3722078.796257/100‑1 (MQ=60)
CCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGT < SRR3722078.537530/100‑1 (MQ=60)
CCAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGT > SRR3722078.1457692/1‑100 (MQ=60)
CAATATGTCGCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGAC < SRR3722078.1082409/100‑1 (MQ=60)
GCCAGAATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGTCGAGTTGGTC > SRR3722078.1388468/1‑100 (MQ=60)
ATGTGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGTCGAGTTGGTCGAAAAA < SRR3722078.482363/100‑1 (MQ=60)
|
CATGGCGTGGTGGGGAAATTCGTCGAATTTTATGGTGATGGTCTGGATTCACTACCGTTGGCGGATCGCGCCACCATTGCCAATATGTCGCCAGAATATGGTGCCACCTGTGGCTTCTTCCCAATCGATGCTGTAACCCTCGATTACATGCGTTTAAGCGGGCGCAGCGAAGATCAGGTCGAGTTGGTCGAAAAA > NZ_CP009273/1330919‑1331113
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
