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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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%
| 142.1
/ NA
| 41 | S276P (TCA→CCA) | yfjI | YfjI family protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/17); total (24/17) |
AAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > NZ_CP009273/2753084‑2753250
|
aaaGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCaaa > 2:512118/1‑90 (MQ=255)
gattggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACa > 1:779458/1‑90 (MQ=255)
gattggattTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACa > 1:42459/1‑90 (MQ=255)
attTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGcc < 2:218368/90‑1 (MQ=255)
ttttttGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCg > 2:189729/1‑90 (MQ=255)
ttttttGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCg < 1:1073870/90‑1 (MQ=255)
ttttttGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCg < 1:296046/90‑1 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:474149/90‑1 (MQ=255)
tGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:26271/90‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTGACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:704943/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCGACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 2:874311/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAATCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:310614/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa < 2:715769/81‑1 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCaa > 1:715769/1‑81 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:1045067/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:446012/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 2:761820/1‑90 (MQ=255)
tgCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATg > 1:1226999/1‑90 (MQ=255)
ccAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGa > 2:1087924/1‑90 (MQ=255)
cAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaa < 2:279753/90‑1 (MQ=255)
cAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaa < 2:1012849/90‑1 (MQ=255)
cAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaa < 1:883261/90‑1 (MQ=255)
cAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaa < 1:634059/90‑1 (MQ=255)
aGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGaaa > 1:464048/1‑90 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTc < 2:1023564/71‑1 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTc > 1:1023564/1‑71 (MQ=255)
gCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAt < 1:229556/90‑1 (MQ=255)
ccTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAAtt > 2:927933/1‑90 (MQ=255)
gCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCa > 1:490585/1‑71 (MQ=255)
gCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCa < 2:490585/71‑1 (MQ=255)
cAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATg < 1:415972/90‑1 (MQ=255)
acacAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATgag > 2:1195656/1‑90 (MQ=255)
acacAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATgag > 2:719195/1‑90 (MQ=255)
acacAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATgag > 2:811313/1‑90 (MQ=255)
aGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGcat > 2:138584/1‑90 (MQ=255)
aCAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTa > 2:432275/1‑90 (MQ=255)
aaaaTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGc < 1:805962/78‑1 (MQ=255)
aaaaTTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGc > 2:805962/1‑78 (MQ=255)
tttCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATg < 1:138584/90‑1 (MQ=255)
tttCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATg < 2:103004/90‑1 (MQ=255)
cAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATc > 1:1152218/1‑90 (MQ=255)
|
AAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > NZ_CP009273/2753084‑2753250
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG > NZ_CP009273/2753080‑2753251
|
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACA > SRR3722089.790065/1‑100 (MQ=60)
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACA > SRR3722089.42988/1‑100 (MQ=60)
TTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACC < SRR3722089.1090010/100‑1 (MQ=60)
TTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACC < SRR3722089.299824/100‑1 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTGACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.714128/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAATCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.314546/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.1060720/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.725075/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.451360/1‑100 (MQ=60)
GTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATG > SRR3722089.1245643/1‑100 (MQ=60)
CTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAA > SRR3722089.469590/1‑100 (MQ=60)
TCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTctgactctt > SRR3722089.1038831/1‑91 (MQ=60)
GTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGctgtctctt > SRR3722089.496400/1‑91 (MQ=60)
CAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATG < SRR3722089.642130/100‑1 (MQ=60)
CAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATG < SRR3722089.895991/100‑1 (MQ=60)
GCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAG < SRR3722089.232470/100‑1 (MQ=60)
CAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCAT < SRR3722089.421004/100‑1 (MQ=60)
agAGGTAACAGAAAAATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAA < SRR3722089.817174/98‑1 (MQ=60)
ATTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATC > SRR3722089.1169756/1‑100 (MQ=60)
TTTCCAACCCAATTTTTCCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG < SRR3722089.140270/100‑1 (MQ=60)
|
TGGCAAAGGGGATTGGATTTTTTGCACGGTGCCTCATGTGCCAGCCTGCTTCAACACAAGGTAACAGAAAAATTTCCAACCCAATTTTTTCAAATGAACATTTGCCGGTATTTCACCAACGTCTTATGGAAATTGTTAATGAGAGCATCATTAAAATTAATGAAAATAATCG > NZ_CP009273/2753080‑2753251
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
