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 F3 I95 R1
|
196 |
14.2 |
808436 |
96.0% |
776098 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,613,753 |
(A)6→5 |
coding (377/435 nt) |
marR → |
multiple antibiotic resistance transcriptional regulator MarR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,613,748 | 0 | A | . | 92.3%
| 40.4
/ ‑0.7
| 13 | coding (372/435 nt) | marR | multiple antibiotic resistance transcriptional regulator MarR |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (8/4); total (8/5) |
| Fisher's exact test for biased strand distribution p-value = 3.85e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.40e-01 |
AACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAG > NZ_CP009273/1613672‑1613822
|
aaCTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGAcggc > 2:36610/1‑90 (MQ=255)
ttACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGa > 2:250454/1‑90 (MQ=255)
accaccGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACg > 1:363528/1‑90 (MQ=255)
accaccGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACg > 2:316769/1‑90 (MQ=255)
gcggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGc < 1:129172/90‑1 (MQ=255)
ggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCa < 1:3473/90‑1 (MQ=255)
gcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAac < 1:283998/90‑1 (MQ=255)
aTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt > 1:300480/1‑82 (MQ=255)
aTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 2:300480/82‑1 (MQ=255)
aTCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGt > 1:293272/1‑90 (MQ=255)
aGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCg > 2:191228/1‑90 (MQ=255)
cTGCACAAAGAATTAAC‑AAAACCCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAaga < 2:129000/90‑1 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 2:252725/1‑90 (MQ=255)
|
AACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAG > NZ_CP009273/1613672‑1613822
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATAC > NZ_CP009273/1613667‑1613847
|
GGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACG > SRR3722235.368761/1‑100 (MQ=60)
GCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAG < SRR3722235.130665/100‑1 (MQ=60)
GGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGT < SRR3722235.3510/100‑1 (MQ=60)
GCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAT < SRR3722235.287917/100‑1 (MQ=60)
TATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAG > SRR3722235.304690/1‑100 (MQ=60)
GAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGT > SRR3722235.297359/1‑100 (MQ=60)
CAAAACCCTGACGGCGGACGAAGTGGCACCACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATAC < SRR3722235.253692/100‑1 (MQ=60)
|
GGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATAC > NZ_CP009273/1613667‑1613847
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
