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 |
1,897,230 |
A→G |
D309G (GAT→GGT) |
manX → |
PTS mannose transporter subunit IIAB |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,897,230 | 0 | A | G | 95.6%
| 148.8
/ 0.8
| 45 | coding (926/972 nt) | manX | PTS mannose transporter subunit IIAB |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (18/25); minor base . (1/1); total (19/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
GGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACT > NZ_CP009273/1897150‑1897310
|
ggTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACC‑‑TCCGAAACTGa > 1:387196/1‑90 (MQ=255)
gatgaAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGaaa < 2:606902/90‑1 (MQ=255)
gatgaAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGaaa < 2:1131124/90‑1 (MQ=255)
aaaaGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat < 1:192705/90‑1 (MQ=255)
aaaaGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACC‑‑TCCGAAACTGAAAATGATgg < 2:387196/90‑1 (MQ=255)
atatCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATc < 2:1080362/90‑1 (MQ=255)
tCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGa < 2:304302/90‑1 (MQ=255)
gAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGa < 1:425631/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat > 1:1029454/1‑67 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAatgat < 2:1029454/67‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 1:308396/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 2:363045/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 2:455872/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa < 2:500095/90‑1 (MQ=255)
aaCTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATa > 1:231055/1‑90 (MQ=255)
gAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTa > 2:846329/1‑90 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 1:479612/90‑1 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 1:98715/90‑1 (MQ=255)
aaTGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTaa < 1:81966/90‑1 (MQ=255)
gcgcgGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAt > 2:449356/1‑90 (MQ=255)
gcgcgGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAt < 1:105420/90‑1 (MQ=255)
gTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTgtgt < 2:991905/90‑1 (MQ=255)
aTTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTg < 2:1061959/90‑1 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGGTGGATCTTTTCAGCAAAAGCGATAAGGAACGAAGTTTGTTGATTATCAc > 2:703164/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGAt > 2:260242/1‑46 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGAt < 1:260242/46‑1 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACg < 2:240995/72‑1 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACg > 1:240995/1‑72 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:681143/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:1043530/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:1209105/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:273563/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:307238/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 1:447240/1‑90 (MQ=255)
ggAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAc > 2:253313/1‑90 (MQ=255)
gAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACt < 1:449356/90‑1 (MQ=255)
aaGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTc > 1:1034275/1‑90 (MQ=255)
aGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCa < 2:55831/90‑1 (MQ=255)
ccGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCa < 2:604532/87‑1 (MQ=255)
ccGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCa > 1:604532/1‑87 (MQ=255)
aGGTTTCCACCGGTCCGAAGCTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTcac < 1:505861/90‑1 (MQ=255)
aGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTcac < 2:953656/90‑1 (MQ=255)
tttCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACt > 2:275033/1‑90 (MQ=255)
ttCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGa < 2:726456/48‑1 (MQ=255)
ttCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGa > 1:726456/1‑48 (MQ=255)
|
GGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACT > NZ_CP009273/1897150‑1897310
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AGGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCT > NZ_CP009273/1897131‑1897317
|
AGGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGG < SRR3722089.298458/100‑1 (MQ=60)
GGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGT > SRR3722089.84795/1‑100 (MQ=60)
ACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACC‑‑TCCGAAACTGA > SRR3722089.391915/1‑100 (MQ=60)
AAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATC < SRR3722089.195127/100‑1 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacaGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCA < SRR3722089.263579/67‑1 (MQ=60)
GCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCctgtctcttatac > SRR3722089.1044830/1‑87 (MQ=60)
GCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATA > SRR3722089.233984/1‑100 (MQ=60)
gacagTGAATGCGCGCGCTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGT < SRR3722089.331792/95‑1 (MQ=60)
GAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGT < SRR3722089.430771/100‑1 (MQ=60)
AACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTAT < SRR3722089.312305/100‑1 (MQ=60)
AATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGT < SRR3722089.99945/100‑1 (MQ=60)
AATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGT < SRR3722089.82965/100‑1 (MQ=60)
AATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGT < SRR3722089.485315/100‑1 (MQ=60)
GCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATT < SRR3722089.106719/100‑1 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGctgtctct > SRR3722089.244060/1‑92 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.311132/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.277052/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.452604/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.1227486/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.689992/1‑100 (MQ=60)
GTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCAC > SRR3722089.1059157/1‑100 (MQ=60)
ATTGAGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTC > SRR3722089.1049733/1‑100 (MQ=60)
AGCTGGAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCATTT > SRR3722089.612000/1‑100 (MQ=60)
GAAGTCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCAC < SRR3722089.454747/100‑1 (MQ=60)
TCCGTAAGGTTTCCACCGGTCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTctgtctcttatacacatctgacgctgccgacg > SRR3722089.735908/1‑68 (MQ=60)
AGGTTTCCACCGGTCCGAAGCTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCT < SRR3722089.511825/100‑1 (MQ=60)
|
AGGTGAATAACGCGGTTTCGGTTGATGAAAAAGATATCGAGGCGTTCAAGAAACTGAATGCGCGCGGTATTGAGCTGGAAGTCCGTAAGGTTTCCACCGATCCGAAACTGAAAATGATGGATCTGATCAGCAAAATCGATAAGTAACGTATTGTGTTGATTATCACTCAGTTTTCACACTTAAGTCT > NZ_CP009273/1897131‑1897317
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
