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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,753,169 |
T→C |
S276P (TCA→CCA) |
yfjI → |
YfjI family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,753,169 | 0 | T | C | 100.0%
| 80.0
/ NA
| 25 | S276P (TCA→CCA) | yfjI | YfjI family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/10); total (15/10) |
CAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > NZ_CP009273/2753083‑2753250
|
cAAAGGGGACTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCaa > 1:243011/1‑90 (MQ=255)
aaGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAAt > 2:90543/1‑90 (MQ=255)
aaGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAAt > 2:249595/1‑90 (MQ=255)
gattggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACa > 2:157698/1‑90 (MQ=255)
attTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGcc < 2:133509/90‑1 (MQ=255)
attTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGcc < 1:423795/90‑1 (MQ=255)
ttttttGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCg < 2:458804/90‑1 (MQ=255)
cACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTc > 2:309253/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTc > 2:259521/1‑76 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTc < 1:259521/76‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:515109/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:346981/1‑90 (MQ=255)
aGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaaa > 1:458744/1‑90 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt < 2:367109/90‑1 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt < 1:251991/90‑1 (MQ=255)
gCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCtt > 1:467449/1‑78 (MQ=255)
gCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCtt < 2:467449/78‑1 (MQ=255)
aGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGcat < 2:195661/90‑1 (MQ=255)
aGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGcat > 2:129469/1‑90 (MQ=255)
aCAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTa > 2:571261/1‑90 (MQ=255)
aaaaTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAAtt > 2:315937/1‑90 (MQ=255)
aaTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTaa > 1:60571/1‑90 (MQ=255)
tCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGaa < 2:44575/90‑1 (MQ=255)
aCCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAaata < 1:315937/90‑1 (MQ=255)
cAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATc > 1:542803/1‑90 (MQ=255)
|
CAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > NZ_CP009273/2753083‑2753250
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
GGAGATATGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCGCATCTG > NZ_CP009273/2753073‑2753257
|
GGAGATATGGCAAAGGGGACTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAA > SRR3722109.245869/1‑100 (MQ=60)
ATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCAC < SRR3722109.430032/100‑1 (MQ=60)
acaGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCT < SRR3722109.262666/97‑1 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722109.351636/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722109.522935/1‑100 (MQ=60)
CTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAA > SRR3722109.465622/1‑100 (MQ=60)
GTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGCT > SRR3722109.474484/1‑100 (MQ=60)
GCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAG < SRR3722109.254974/100‑1 (MQ=60)
GTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAA > SRR3722109.61295/1‑100 (MQ=60)
ATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > SRR3722109.551041/1‑100 (MQ=60)
ACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCGCATCTG < SRR3722109.320095/100‑1 (MQ=60)
|
GGAGATATGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCGCATCTG > NZ_CP009273/2753073‑2753257
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
