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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,335,990 |
A→T |
intergenic (+6/‑188) |
lapB → / → pyrF |
lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,335,990 | 0 | A | T | 81.2%
| 36.3
/ 4.2
| 16 | intergenic (+6/‑188) | lapB/pyrF | lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
| Reads supporting (aligned to +/- strand): ref base A (1/2); new base T (7/6); total (8/8) |
| 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 |
ATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGAC > NZ_CP009273/1335906‑1336054
|
aTACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTtaaaaa > 2:685912/1‑90 (MQ=255)
cccTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATcc > 1:327978/1‑90 (MQ=255)
ctACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACt > 1:643508/1‑90 (MQ=255)
ctACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACt > 2:355072/1‑90 (MQ=255)
ggCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGt < 2:556751/90‑1 (MQ=255)
gCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGtt > 1:389416/1‑90 (MQ=255)
aTTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTac < 1:611220/90‑1 (MQ=255)
gTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATAc < 2:626496/90‑1 (MQ=255)
gTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATAc < 2:327978/90‑1 (MQ=255)
cTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTa < 1:189757/90‑1 (MQ=255)
aaCCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCAt < 2:449791/90‑1 (MQ=255)
aCCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCAtt > 2:529660/1‑90 (MQ=255)
tAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCt > 2:605748/1‑90 (MQ=255)
gATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCa > 2:465469/1‑90 (MQ=255)
gcgGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAacgac < 2:621541/90‑1 (MQ=255)
tGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAacgac < 1:417900/75‑1 (MQ=255)
tGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAacgac > 2:417900/1‑75 (MQ=255)
|
ATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGAC > NZ_CP009273/1335906‑1336054
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
ACCGCATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAA > NZ_CP009273/1335901‑1336064
|
ACCGCATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCC > SRR3722073.334947/1‑100 (MQ=60)
CATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACT > SRR3722073.656776/1‑100 (MQ=60)
CCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTT > SRR3722073.397707/1‑100 (MQ=60)
ATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAA < SRR3722073.623948/100‑1 (MQ=60)
CTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATG < SRR3722073.193511/100‑1 (MQ=60)
gacagCTTGATGGCCTGTAATTTTTTAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAA < SRR3722073.426838/95‑1 (MQ=60)
|
ACCGCATACACCCTCTACTGGCATTGTCCGTCTTGTCGGGCCTGGTCAACCATTAAACCGATTCGCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAA > NZ_CP009273/1335901‑1336064
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
