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 I229 R1
|
214 |
17.4 |
943020 |
97.5% |
919444 |
87.1 |
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%
| 64.2
/ NA
| 18 | G103G (GGA→GGT) | yfcC | putative basic amino acid antiporter YfcC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (8/10); total (8/10) |
TATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAC > NZ_CP009273/2410788‑2410951
|
tATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATAc < 1:324096/90‑1 (MQ=255)
aCCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGa > 2:155710/1‑90 (MQ=255)
ccGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGAc < 1:391698/90‑1 (MQ=255)
aCAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGt < 1:421204/90‑1 (MQ=255)
cAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGtt < 2:288088/90‑1 (MQ=255)
gCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTgg > 1:436174/1‑90 (MQ=255)
gTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcat > 1:77982/1‑90 (MQ=255)
acgacgGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGcatcatc < 2:308219/90‑1 (MQ=255)
gCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGa > 2:116892/1‑90 (MQ=255)
gggCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTgg > 1:136431/1‑90 (MQ=255)
gggCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTgg > 2:420958/1‑90 (MQ=255)
aaCTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGttt < 2:466250/90‑1 (MQ=255)
tCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCa > 1:72196/1‑90 (MQ=255)
gAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATg < 2:136431/90‑1 (MQ=255)
aaGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGc < 1:254074/90‑1 (MQ=255)
ttAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACa > 1:62233/1‑90 (MQ=255)
aCCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGa < 2:405396/90‑1 (MQ=255)
cTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAc < 1:95630/90‑1 (MQ=255)
|
TATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAC > NZ_CP009273/2410788‑2410951
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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
GAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAAC > NZ_CP009273/2410770‑2410961
|
GAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTT < SRR3722113.288664/100‑1 (MQ=60)
TATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCG < SRR3722113.327316/100‑1 (MQ=60)
ACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGG > SRR3722113.440791/1‑100 (MQ=60)
CCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGC < SRR3722113.395802/100‑1 (MQ=60)
GCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCAT > SRR3722113.78665/1‑100 (MQ=60)
ACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATC < SRR3722113.425656/100‑1 (MQ=60)
ATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGG > SRR3722113.137574/1‑100 (MQ=60)
CTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCA > SRR3722113.72829/1‑100 (MQ=60)
GTTTGAAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACA > SRR3722113.62783/1‑100 (MQ=60)
AAGGATTAACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAAC < SRR3722113.256290/100‑1 (MQ=60)
AACCTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGAT > SRR3722113.399660/1‑100 (MQ=60)
CTCAGGTTCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAAC < SRR3722113.96491/100‑1 (MQ=60)
|
GAAGCAGGCGAACCTGAGTATCACCGCGTACAGCTGTTCACGACGGGCGATGAACGCCCGGGCCTGATGAACTTCCCGTTTGAAGGATTAACCTCAGGATCGAAATACGGGACAGCCGTTGGCATCATCATGTTTATGCTGGTGATTGGCGGCGCGTTTGGCATTGTGATGCGTACAGGAACCATTGATAAC > NZ_CP009273/2410770‑2410961
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
