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 I96 R1
|
172 |
34.7 |
2005794 |
96.2% |
1929573 |
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 | . | 95.8%
| 90.6
/ ‑1.4
| 24 | coding (372/435 nt) | marR | multiple antibiotic resistance transcriptional regulator MarR |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base . (10/13); total (11/13) |
| Fisher's exact test for biased strand distribution p-value = 4.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
GGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG > NZ_CP009273/1613659‑1613833
|
ggcgTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACa > 1:155369/1‑90 (MQ=255)
cTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACaaaaacc > 1:233781/1‑88 (MQ=255)
cTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACaaaaacc > 1:129976/1‑88 (MQ=255)
ttACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGa > 2:654505/1‑90 (MQ=255)
tACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGa > 2:426734/1‑90 (MQ=255)
accaccGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACg > 2:981672/1‑90 (MQ=255)
caccGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGaa < 2:119301/90‑1 (MQ=255)
accGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAg < 1:594229/90‑1 (MQ=255)
gcggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGc < 2:122362/90‑1 (MQ=255)
cggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCa < 1:313312/90‑1 (MQ=255)
cggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCa < 1:654505/90‑1 (MQ=255)
cggcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCa < 1:663062/90‑1 (MQ=255)
gcgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAac < 2:696186/90‑1 (MQ=255)
cgcggcAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAaca < 1:146245/90‑1 (MQ=255)
tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 2:984001/90‑1 (MQ=255)
tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 1:58108/90‑1 (MQ=255)
tgtgAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTAtt < 1:548506/90‑1 (MQ=255)
atgtcATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAg > 2:209180/5‑90 (MQ=255)
aTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGTCGAAAAGGCAAGCCTTGATTTTTTACTTAAg > 1:633414/1‑90 (MQ=255)
aTGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAg > 1:988827/1‑90 (MQ=255)
aTCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGt > 1:696587/1‑90 (MQ=255)
gCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAAc < 2:96206/90‑1 (MQ=255)
ggACCTGCTCCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGAATTTGCTTAAGAAAGTCCTGCCGTAAACaaaa > 1:815229/1‑90 (MQ=255)
tGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAagag > 2:236565/1‑90 (MQ=255)
cAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATg > 1:622010/1‑90 (MQ=255)
aaTTAAC‑AAAACCCTGACGGCGGACGAAGGGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGa < 1:809878/90‑1 (MQ=255)
ttAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATg > 2:109915/1‑90 (MQ=255)
|
GGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATG > NZ_CP009273/1613659‑1613833
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 30 ≤ 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
GCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATACTGACG > NZ_CP009273/1613655‑1613852
|
GCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAACC > SRR3722236.131830/1‑100 (MQ=60)
GCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAACC > SRR3722236.237258/1‑100 (MQ=60)
ACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACT < SRR3722236.603573/100‑1 (MQ=60)
CGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGT < SRR3722236.317820/100‑1 (MQ=60)
CGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGT < SRR3722236.674057/100‑1 (MQ=60)
CGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGT < SRR3722236.665332/100‑1 (MQ=60)
CGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATT < SRR3722236.148372/100‑1 (MQ=60)
TATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGtcgaaaaggcaagccttgattttttacttaag > SRR3722236.643740/1‑68 (MQ=60)
TATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAG > SRR3722236.1006249/1‑100 (MQ=60)
TGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAA < SRR3722236.58926/100‑1 (MQ=60)
TGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAA < SRR3722236.556958/100‑1 (MQ=60)
GAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGT > SRR3722236.708331/1‑100 (MQ=60)
TAGTTGGCCAGGACCTGCTCCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGAATTTGCTTAAGAAAGTCCTGCCGTAAACAAAA > SRR3722236.829425/1‑100 (MQ=60)
GGACCTGCACCAAGAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATG > SRR3722236.632063/1‑100 (MQ=60)
GAATTAAC‑AAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAActgtctcttatacacatctgacgctgccgacgaaggcttagg > SRR3722236.582612/1‑58 (MQ=60)
AATTAAC‑AAAACCCTGACGGCGGACGAAGGGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACG < SRR3722236.823952/100‑1 (MQ=60)
ACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATACTGACG < SRR3722236.430989/100‑1 (MQ=60)
|
GCGCGGCGTACTGGTAAAACTTACCACCGGCGGCGCGGCAATATGTGAACAATGCCATCAATTAGTTGGCCAGGACCTGCACCAAGAATTAACAAAAAACCTGACGGCGGACGAAGTGGCAACACTTGAGTATTTGCTTAAGAAAGTCCTGCCGTAAACAAAAAAGAGGTATGACGATGTCCAGACGCAATACTGACG > NZ_CP009273/1613655‑1613852
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
