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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,543,103 |
A→G |
E129G (GAA→GGA) |
uxuB → |
fructuronate reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,543,103 | 0 | A | G | 88.9%
| 42.9
/ 0.1
| 18 | E129G (GAA→GGA) | uxuB | fructuronate reductase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (7/9); total (8/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
CCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTG > NZ_CP009273/4543024‑4543186
|
ccGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTAc < 2:468628/90‑1 (MQ=255)
aaTCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTgcgc < 2:376218/90‑1 (MQ=255)
ggTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGt < 1:478284/90‑1 (MQ=255)
tctcAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACt > 2:383822/1‑90 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc > 1:274111/1‑90 (MQ=255)
aCGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAtc > 2:449461/1‑90 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGc < 1:148234/72‑1 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGc > 2:148234/1‑72 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg < 1:189200/74‑1 (MQ=255)
aTGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCgg > 2:189200/1‑74 (MQ=255)
tGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATa < 1:308478/90‑1 (MQ=255)
gcgTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATTCGGCAAGCGGTCAACTGGATCTCAATAAccc > 2:470079/1‑90 (MQ=255)
cGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACg > 1:192754/1‑90 (MQ=255)
gATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGa < 2:126972/90‑1 (MQ=255)
tGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCt < 2:274111/90‑1 (MQ=255)
cGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGa > 2:438135/1‑90 (MQ=255)
ggTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGAc < 1:383822/90‑1 (MQ=255)
tCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTg < 1:438135/90‑1 (MQ=255)
|
CCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTG > NZ_CP009273/4543024‑4543186
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
GATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGC > NZ_CP009273/4543005‑4543199
|
GATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGA < SRR3722087.174989/100‑1 (MQ=60)
AAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGG < SRR3722087.130200/100‑1 (MQ=60)
agagacagTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGG < SRR3722087.149600/92‑1 (MQ=60)
agacagTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGAT < SRR3722087.190865/94‑1 (MQ=60)
GGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATC > SRR3722087.276818/1‑100 (MQ=60)
GGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATC < SRR3722087.483855/100‑1 (MQ=60)
TGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGAT < SRR3722087.311713/100‑1 (MQ=60)
CCGCAAACGGCGATTGTCTCTCTAACGGTCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACG > SRR3722087.194449/1‑100 (MQ=60)
GGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAG < SRR3722087.388246/100‑1 (MQ=60)
TCACGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTC < SRR3722087.443260/100‑1 (MQ=60)
CGGGAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGC > SRR3722087.53688/1‑100 (MQ=60)
|
GATGAAAGAAGCGCTGCATCCGGAAATCGATGGCTGCGAAGGTATTCTCAACGCGATGGCGCGTCCGCAAACGGCGATTGTCTCTCTAACGGTCACGGAAAAAGGCTACTGCGCTGATGCGGCAAGCGGTCAACTGGATCTCAATAACCCGCTGATCAAGCACGATCTGGAAAACCCGACTGCGCCGAAGTCCGC > NZ_CP009273/4543005‑4543199
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
