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 |
2,122,528 |
T→G |
T202P (ACC→CCC) |
wcaE ← |
colanic acid biosynthesis glycosyltransferase WcaE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,122,528 | 0 | T | G | 86.4%
| 63.5
/ 3.1
| 22 | T202P (ACC→CCC) | wcaE | colanic acid biosynthesis glycosyltransferase WcaE |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base G (11/8); total (12/10) |
| Fisher's exact test for biased strand distribution p-value = 5.71e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.44e-01 |
ATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAG > NZ_CP009273/2122447‑2122612
|
aTTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATAccc < 2:196455/90‑1 (MQ=255)
cccAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACcccaccca > 1:166501/1‑90 (MQ=255)
aaGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGaa < 2:33594/90‑1 (MQ=255)
aaGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGaa < 2:151423/90‑1 (MQ=255)
gCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAg < 1:781186/90‑1 (MQ=255)
gCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAg < 2:274036/90‑1 (MQ=255)
aTGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGacac > 1:321504/1‑90 (MQ=255)
ttGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGTTGGGAGAAACCCCACCCATGGAAAATTCAGACACCAGGCCAtt > 1:281757/1‑90 (MQ=255)
ttGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATGCAGACACCAGGCCAtt > 2:639562/1‑90 (MQ=255)
gTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGa < 1:35491/90‑1 (MQ=255)
ggACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAg < 2:734771/45‑1 (MQ=255)
ttttCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATg < 2:166501/90‑1 (MQ=255)
gTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAAcc > 1:685428/1‑90 (MQ=255)
tCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCg < 1:647694/90‑1 (MQ=255)
caATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTtata > 2:69420/1‑90 (MQ=255)
ccATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACAttt > 1:120933/1‑90 (MQ=255)
ttattGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCt > 2:882998/1‑90 (MQ=255)
ttattGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCt > 1:576710/1‑90 (MQ=255)
attGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTa < 2:448933/58‑1 (MQ=255)
attGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTa > 1:448933/1‑58 (MQ=255)
attGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGc > 1:304755/1‑90 (MQ=255)
attGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGc > 1:892388/1‑90 (MQ=255)
ggtgggAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAg > 1:392863/1‑90 (MQ=255)
|
ATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAG > NZ_CP009273/2122447‑2122612
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ 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
GTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAGCGCGTAGTCGGAAG > NZ_CP009273/2122432‑2122626
|
GTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGA < SRR3722072.754221/100‑1 (MQ=60)
GATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCA > SRR3722072.169386/1‑100 (MQ=60)
agcagaagacggcatacgagataatcggacgtctcgtgggcccggagatgtgtataagagacagTCCATATTATTGGTGGGAGATACCCCACCCATGGAA < SRR3722072.628369/36‑1 (MQ=60)
atacgagataatcggacgtctcgtgggctcggagatgtgtataagagaCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTC < SRR3722072.528822/52‑1 (MQ=60)
AGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACAC > SRR3722072.327121/1‑100 (MQ=60)
GCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCC < SRR3722072.794887/100‑1 (MQ=60)
CATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGTTGGGAGAAACCCCACCCATGGAAAATTCAGACACCAGGCCATT > SRR3722072.286578/1‑100 (MQ=60)
ATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCtgtctcttatacacatctccgagcccacgagacg > SRR3722072.747808/1‑66 (MQ=60)
GTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAA < SRR3722072.36124/100‑1 (MQ=60)
CTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACC > SRR3722072.697695/1‑100 (MQ=60)
TCAGCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACA < SRR3722072.659257/100‑1 (MQ=60)
GCACACAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTT > SRR3722072.123138/1‑100 (MQ=60)
CAATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCT > SRR3722072.587009/1‑100 (MQ=60)
ATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCtgtctcttatacacatctccg > SRR3722072.457153/1‑79 (MQ=60)
ATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGC > SRR3722072.310036/1‑100 (MQ=60)
ATTCCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGC > SRR3722072.907750/1‑100 (MQ=60)
CCATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAG > SRR3722072.399926/1‑100 (MQ=60)
ATATTATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAGCG > SRR3722072.797773/1‑100 (MQ=60)
ATTGGTGGGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAGCGCGTAG > SRR3722072.348215/1‑100 (MQ=60)
GGAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAGCGCGTAGTCGGAAG > SRR3722072.436506/1‑100 (MQ=60)
|
GTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTTTTCGCGTCAGCACACAATTCCATATTATTGGTGGTAGATACCCCACCCATGGAAAATTCAGACACCAGGCCATTGAGTTTTTTAAATGCATAACCGGCTTTATACATTTTGGCTGCCAGCGCGTAGTCGGAAG > NZ_CP009273/2122432‑2122626
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
