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 I201 R1
|
4 |
35.3 |
1949590 |
96.5% |
1881354 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,610,344 |
T→C |
W309R (TGG→CGG) |
deoB → |
phosphopentomutase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,610,344 | 0 | T | C | 81.8%
| 109.0
/ 24.4
| 55 | W309R (TGG→CGG) | deoB | phosphopentomutase |
| Reads supporting (aligned to +/- strand): ref base T (4/6); new base C (31/14); total (35/20) |
| Fisher's exact test for biased strand distribution p-value = 1.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01 |
CGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCT > NZ_CP009273/4610258‑4610421
|
cgcTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTggg > 2:561326/1‑90 (MQ=255)
cgcTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCggg > 2:608819/1‑90 (MQ=255)
cgcTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCggg > 2:110987/1‑90 (MQ=255)
gcTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCgggg > 2:100437/1‑90 (MQ=255)
gcTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCgggg > 1:712429/1‑90 (MQ=255)
cTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGc < 2:724707/90‑1 (MQ=255)
tGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGcc < 2:569383/90‑1 (MQ=255)
tttGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCAc > 1:723197/1‑90 (MQ=255)
accaTCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGa < 1:201104/89‑1 (MQ=255)
accaTCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGa > 2:201104/1‑89 (MQ=255)
accaTCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGAc > 2:935265/1‑90 (MQ=255)
accaTCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGAc > 1:955560/1‑90 (MQ=255)
tCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCg < 1:62211/90‑1 (MQ=255)
aaaGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGcc < 1:362432/90‑1 (MQ=255)
gaTGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTa > 2:428472/1‑90 (MQ=255)
gaTGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTa > 2:143943/1‑90 (MQ=255)
gaTGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTa > 2:589782/1‑90 (MQ=255)
gaagCGGGTGATACCACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg < 1:471254/90‑1 (MQ=255)
gaagCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg < 1:681671/90‑1 (MQ=255)
aagCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCgg > 1:411775/1‑90 (MQ=255)
gCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGt > 2:326868/1‑90 (MQ=255)
gCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGt > 2:663777/1‑90 (MQ=255)
gCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGt > 1:361064/1‑90 (MQ=255)
cGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTc > 1:870254/1‑90 (MQ=255)
tGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGa < 2:688979/90‑1 (MQ=255)
cacCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGtt > 1:406929/1‑90 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg > 2:746513/1‑74 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg < 1:746513/74‑1 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCg > 1:874867/1‑90 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCg > 2:604598/1‑90 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCg > 2:786571/1‑90 (MQ=255)
ccATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCg > 2:253534/1‑90 (MQ=255)
ccATCGTCTTCACCAACTTCGTCGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCg > 2:279428/1‑90 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg < 2:721902/72‑1 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCcgcg > 1:721902/1‑72 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTc < 1:621197/76‑1 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTc > 2:621197/1‑76 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAc > 1:394092/1‑90 (MQ=255)
aTCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAc > 1:375333/1‑90 (MQ=255)
tCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAcc > 1:889746/1‑90 (MQ=255)
gTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAccgc < 2:467531/90‑1 (MQ=255)
gTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAccgc < 1:663902/90‑1 (MQ=255)
cTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAccgccg > 2:161448/1‑90 (MQ=255)
ttCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGt < 1:663777/90‑1 (MQ=255)
cAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGcc < 2:889746/90‑1 (MQ=255)
cAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGcc < 2:212820/90‑1 (MQ=255)
aCTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCgg > 1:441230/1‑90 (MQ=255)
tCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGc < 2:874867/90‑1 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACt > 2:155156/1‑65 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACt < 1:155156/65‑1 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGc > 1:895149/1‑88 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGc < 2:895149/88‑1 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTg > 2:695538/1‑90 (MQ=255)
gTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTg < 2:870254/90‑1 (MQ=255)
ttCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGtct > 2:63896/1‑90 (MQ=255)
|
CGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCT > NZ_CP009273/4610258‑4610421
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 33 ≤ 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
GCCTGGACGCGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCTCTGCTGCGCGATGACGACA > NZ_CP009273/4610249‑4610440
|
GCCTGGACGCGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGG > SRR3722083.723781/1‑100 (MQ=60)
GGACGCGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCAC > SRR3722083.734758/1‑100 (MQ=60)
GACGCGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACC < SRR3722083.567648/100‑1 (MQ=60)
GTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGAC > SRR3722083.971241/1‑100 (MQ=60)
CACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGT < SRR3722083.203906/100‑1 (MQ=60)
CCATCAAAGAGATGAAAGAAGCGGGGGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACnnnnnnnnnnnnnnnnnnnn > SRR3722083.587836/1‑80 (MQ=60)
TCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGC < SRR3722083.63049/100‑1 (MQ=60)
AAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCG < SRR3722083.367248/100‑1 (MQ=60)
GAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGG > SRR3722083.417174/1‑100 (MQ=60)
GATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGT > SRR3722083.365869/1‑100 (MQ=60)
ATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTC > SRR3722083.884537/1‑100 (MQ=60)
agacaGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAAC < SRR3722083.758543/95‑1 (MQ=60)
GAAGCGGGTGATACCACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAAC < SRR3722083.477874/100‑1 (MQ=60)
GAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAAC < SRR3722083.692402/100‑1 (MQ=60)
acaGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAGCTGTT < SRR3722083.630658/97‑1 (MQ=60)
CGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTT > SRR3722083.412275/1‑100 (MQ=60)
GGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCG > SRR3722083.889220/1‑100 (MQ=60)
TGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACctgtctct > SRR3722083.733440/1‑92 (MQ=60)
TGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAC > SRR3722083.380297/1‑100 (MQ=60)
TGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGAC > SRR3722083.399279/1‑100 (MQ=60)
GATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACC > SRR3722083.904369/1‑100 (MQ=60)
gtgtataagagacagCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGC < SRR3722083.157266/85‑1 (MQ=60)
GTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGG < SRR3722083.674267/100‑1 (MQ=60)
GTCTTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGG > SRR3722083.447203/1‑100 (MQ=60)
TTCACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGC < SRR3722083.674136/100‑1 (MQ=60)
CACCAACTTCGTTGACTTCGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTG > SRR3722083.909857/1‑100 (MQ=60)
CGACTCTTCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCTCTGCTGCGCGAT > SRR3722083.878212/1‑100 (MQ=60)
TCCCGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCTCTGCTGCGCGATGACGACA > SRR3722083.561107/1‑100 (MQ=60)
|
GCCTGGACGCGCTGTTTGACGCCACCATCAAAGAGATGAAAGAAGCGGGTGATAACACCATCGTCTTCACCAACTTCGTTGACTTCGACTCTTCCTGGGGCCACCGTCGCGACGTCGCCGGTTATGCCGCGGGTCTGGAACTGTTCGACCGCCGTCTGCCGGAGCTGATGTCTCTGCTGCGCGATGACGACA > NZ_CP009273/4610249‑4610440
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
