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 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
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 | . | 95.8%
| 90.8
/ ‑1.2
| 24 | coding (372/435 nt) | marR | multiple antibiotic resistance transcriptional regulator MarR |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (15/8); total (15/9) |
| Fisher's exact test for biased strand distribution p-value = 3.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01 |
ACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG > NZ_CP009273/1613664‑1613833
|
aCTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACaaaaac > 2:345816/1‑89 (MQ=255)
ttACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGa > 1:593031/1‑90 (MQ=255)
tACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGAc < 2:60763/90‑1 (MQ=255)
tACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGAc < 1:460805/90‑1 (MQ=255)
ggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCaa < 1:152728/90‑1 (MQ=255)
tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 2:593031/90‑1 (MQ=255)
tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 2:122676/90‑1 (MQ=255)
cAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCtt < 1:493690/90‑1 (MQ=255)
aaTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTaa > 1:360110/1‑90 (MQ=255)
tGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGa > 1:137871/1‑90 (MQ=255)
gCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAAc > 2:457168/1‑90 (MQ=255)
ccAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACa > 1:329133/1‑90 (MQ=255)
ggACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 2:545823/61‑1 (MQ=255)
ggACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt > 1:545823/1‑61 (MQ=255)
aCCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACaaaaaa < 2:32384/90‑1 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 2:216222/1‑90 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 1:216701/1‑90 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 1:515175/1‑90 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 1:413979/1‑90 (MQ=255)
gCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAgg > 1:296462/1‑90 (MQ=255)
aaGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGa > 2:30560/1‑90 (MQ=255)
aaGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGa > 2:516633/1‑90 (MQ=255)
aaTTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGa < 1:345816/90‑1 (MQ=255)
aTTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGAt > 2:374179/1‑90 (MQ=255)
ttAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATg > 1:245946/1‑90 (MQ=255)
|
ACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG > NZ_CP009273/1613664‑1613833
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ 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
CTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACG > NZ_CP009273/1613665‑1613841
|
CTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGA > SRR3721989.605924/1‑100 (MQ=60)
TACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAA < SRR3721989.470467/100‑1 (MQ=60)
GGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTA < SRR3721989.155497/100‑1 (MQ=60)
ATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAA > SRR3721989.367071/1‑100 (MQ=60)
ATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGA > SRR3721989.140371/1‑100 (MQ=60)
CAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCC < SRR3721989.504147/100‑1 (MQ=60)
AATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACA > SRR3721989.335403/1‑100 (MQ=60)
TAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAActgtctcttatacacatct > SRR3721989.557598/1‑81 (MQ=60)
GGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAG > SRR3721989.220632/1‑100 (MQ=60)
GGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAG > SRR3721989.422470/1‑100 (MQ=60)
GGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAG > SRR3721989.526172/1‑100 (MQ=60)
GCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGG > SRR3721989.301984/1‑100 (MQ=60)
GCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG > SRR3721989.250331/1‑100 (MQ=60)
AATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACG < SRR3721989.352456/100‑1 (MQ=60)
|
CTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACG > NZ_CP009273/1613665‑1613841
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
