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 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,673,542 |
A→G |
K287E (AAG→GAG) ‡ |
ydgH → |
DUF1471 family protein YdgH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,673,542 | 0 | A | G | 92.3%
| 59.7
/ ‑6.3
| 26 | K287E (AAG→GAG) ‡ | ydgH | DUF1471 family protein YdgH |
| Reads supporting (aligned to +/- strand): ref base A (0/2); new base G (6/18); total (6/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA > NZ_CP009273/1673457‑1673627
|
gatgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCggagaa < 2:888079/90‑1 (MQ=255)
atgGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGaaa < 2:534130/90‑1 (MQ=255)
ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt < 1:795734/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 1:254991/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 1:269367/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 2:767712/90‑1 (MQ=255)
gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa < 2:332697/90‑1 (MQ=255)
aTCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACcac > 2:513374/1‑90 (MQ=255)
ctGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGcc > 1:189004/1‑90 (MQ=255)
aTGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTTCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGt > 1:518329/1‑90 (MQ=255)
aaGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAAcc > 2:918744/1‑90 (MQ=255)
tATCGGGTTGCAAAACGTGCCGGGGAAAAGGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 1:331592/90‑1 (MQ=255)
tATCCGGTTGCAAACCGTGCGGCGAAAAAAGGTTCAAAATATTCCCACAACCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 2:248778/90‑1 (MQ=255)
tATCAGTTTGCAAAGCGTCCGGGGGAAAAAGGTGCTAATTATTCCCACCCCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 2:385855/90‑1 (MQ=255)
tATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 1:718059/90‑1 (MQ=255)
tATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCAAAGTTTTACCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 1:543938/90‑1 (MQ=255)
tATCAGGTTGCAAACCGTGCCGGGGAAAAAGGTGCTAATTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTc < 1:83897/90‑1 (MQ=255)
ggTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc < 1:488006/90‑1 (MQ=255)
ggTTGCAAAACGTGCCGCGGAAAAAGGTGCAAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAgcgc < 1:798222/90‑1 (MQ=255)
tGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCGCAGa > 2:7446/1‑90 (MQ=255)
gcaaaaCGGGCCGCGAAAAAGGGTGTAAATTTTTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGAt < 2:215264/87‑1 (MQ=255)
cGAACCGTGCGGGGGAAAAGGGTGCAAAGTATTCCCACACCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc < 2:189004/90‑1 (MQ=255)
cGAAACGTGCCGGGGAAAGAGGTGATAATTTTTACCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc < 2:513508/90‑1 (MQ=255)
gTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGGGGGAATAACCTGACCGTCAGCGCAGATCTGtata > 1:120445/1‑90 (MQ=255)
tGCCGGGGAAAAAGGTGCAAAGTATTCCCACACCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTataa < 1:729533/90‑1 (MQ=255)
tGCCGCGGAAAAAGGTGCTAATTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTataa < 1:347230/90‑1 (MQ=255)
cgcgGAAAAGGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTataaata < 1:513374/90‑1 (MQ=255)
|
GATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA > NZ_CP009273/1673457‑1673627
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GACCGCAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAC > NZ_CP009273/1673445‑1673640
|
GACCGCAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAG < SRR3722072.515426/100‑1 (MQ=60)
CCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACC < SRR3722072.809658/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722072.259313/100‑1 (MQ=60)
GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC < SRR3722072.273948/100‑1 (MQ=60)
ATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCC > SRR3722072.192284/1‑100 (MQ=60)
CTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTTCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGT > SRR3722072.527660/1‑100 (MQ=60)
CCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACctgtctcttatacacatctccgagcccacgagacgtccgattatctcgta > SRR3722072.64412/1‑50 (MQ=60)
CTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCtgtctcttatacacatctccgagcccacgagacgtccgattatctcgtatgcc > SRR3722072.581724/1‑47 (MQ=60)
TATCGGGTTGCAAAACGTGCCGGGGAAAAGGGTGCTAAGTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC < SRR3722072.337414/100‑1 (MQ=60)
TATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTATTCCCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC < SRR3722072.730837/100‑1 (MQ=60)
TATCAGGTTGCGAAACGTGCCGGGGAAAAAGGTGCAAAGTTTTACCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC < SRR3722072.553724/100‑1 (MQ=60)
TATCAGGTTGCAAACCGTGCCGGGGAAAAAGGTGCTAATTATTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC < SRR3722072.85472/100‑1 (MQ=60)
GGTTGCGAAACGTGCCGGGGAAAAAGGTGCTAAGTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTAT < SRR3722072.496825/100‑1 (MQ=60)
GGTTGCAAAACGTGCCGCGGAAAAAGGTGCAAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTAT < SRR3722072.812179/100‑1 (MQ=60)
GTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGGGGGAATAACCTGACCGTCAGCGCAGATCTGTATA > SRR3722072.122645/1‑100 (MQ=60)
TGCCGCGGAAAAAGGTGCTAATTTTTCCCACATCCCCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTC < SRR3722072.353337/100‑1 (MQ=60)
GGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGGAATAACCTGACCGTCAGCCCAGATCTttatctgtctcttatacacatc > SRR3722072.490149/1‑78 (MQ=60)
|
GACCGCAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATAACTATTCAGTTAC > NZ_CP009273/1673445‑1673640
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
