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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,410,868 |
A→T |
G103G (GGA→GGT) |
yfcC → |
putative basic amino acid antiporter YfcC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,410,868 | 0 | A | T | 100.0%
| 112.2
/ NA
| 30 | G103G (GGA→GGT) | yfcC | putative basic amino acid antiporter YfcC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (13/17); total (13/17) |
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCAT > NZ_CP009273/2410783‑2410954
|
cTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGTCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGa < 1:724366/90‑1 (MQ=255)
cTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGa < 1:224219/90‑1 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 1:284882/1‑90 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 2:442627/1‑90 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 1:427208/1‑90 (MQ=255)
ccGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAc < 1:440051/90‑1 (MQ=255)
ccGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAc < 1:572380/90‑1 (MQ=255)
ccGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAc < 1:180256/90‑1 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 2:602848/1‑90 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 1:543218/1‑90 (MQ=255)
gcgTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAg > 2:273217/1‑90 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca > 2:57267/1‑90 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca < 1:692288/90‑1 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca < 2:510239/90‑1 (MQ=255)
tGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGca < 2:496078/90‑1 (MQ=255)
ttCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatc > 2:729180/1‑90 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 2:609004/90‑1 (MQ=255)
gCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTggcg > 1:602799/1‑90 (MQ=255)
cTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTggcggc < 2:83336/90‑1 (MQ=255)
tgatgaACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGgcggcg < 2:83587/90‑1 (MQ=255)
tgatgaACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGgcggcg < 1:432313/90‑1 (MQ=255)
aCTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGttt > 2:5210/1‑89 (MQ=255)
aCTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGttt < 1:5210/89‑1 (MQ=255)
gAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATg < 2:427208/90‑1 (MQ=255)
gAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATg > 1:416001/1‑90 (MQ=255)
aaGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGc < 2:251036/90‑1 (MQ=255)
cTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAc < 1:442627/90‑1 (MQ=255)
cAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCa < 1:57267/90‑1 (MQ=255)
cAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCa > 1:276030/1‑90 (MQ=255)
aGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCAt > 1:748122/1‑90 (MQ=255)
|
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCAT > NZ_CP009273/2410783‑2410954
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
AACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAACGGTA > NZ_CP009273/2410780‑2410965
|
AACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGG < SRR3722073.354561/100‑1 (MQ=60)
CCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGA > SRR3722073.290920/1‑100 (MQ=60)
CCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGA > SRR3722073.436346/1‑100 (MQ=60)
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGTCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAC < SRR3722073.738989/100‑1 (MQ=60)
CTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAC < SRR3722073.228880/100‑1 (MQ=60)
GAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAG > SRR3722073.554563/1‑100 (MQ=60)
CCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGC < SRR3722073.449458/100‑1 (MQ=60)
CCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGC < SRR3722073.584340/100‑1 (MQ=60)
CCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGC < SRR3722073.183743/100‑1 (MQ=60)
TGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTT < SRR3722073.706378/100‑1 (MQ=60)
GAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCG > SRR3722073.615360/1‑100 (MQ=60)
TGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCAT < SRR3722073.441562/100‑1 (MQ=60)
AACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGA < SRR3722073.5350/100‑1 (MQ=60)
CTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATG > SRR3722073.424890/1‑100 (MQ=60)
GGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCA > SRR3722073.281868/1‑100 (MQ=60)
GATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCAT > SRR3722073.763290/1‑100 (MQ=60)
CTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAAC < SRR3722073.452091/100‑1 (MQ=60)
CAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAACGG < SRR3722073.58621/100‑1 (MQ=60)
GGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTCGGCATTGTGTCGCGTACAGGAACCtgtctcttatcta > SRR3722073.280369/1‑87 (MQ=60)
|
AACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAACGGTA > NZ_CP009273/2410780‑2410965
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
