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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
568,752 |
A→G |
G71G (GGA→GGG) |
ybcO → |
DUF1364 domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 568,752 | 0 | A | G | 95.2%
| 59.8
/ ‑3.4
| 21 | G71G (GGA→GGG) | ybcO | DUF1364 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (5/15); total (6/15) |
| Fisher's exact test for biased strand distribution p-value = 2.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAC > NZ_CP009273/568680‑568838
|
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 2:529411/90‑1 (MQ=255)
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 2:523618/90‑1 (MQ=255)
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 1:335800/90‑1 (MQ=255)
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 1:439145/90‑1 (MQ=255)
ccTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATgcgc < 1:607271/90‑1 (MQ=255)
tGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGa < 2:352983/90‑1 (MQ=255)
gCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCg < 1:638199/90‑1 (MQ=255)
tGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCgaga < 2:112793/90‑1 (MQ=255)
ctgcctgcCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAacac > 1:188459/1‑90 (MQ=255)
ctgcctgcCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAacac > 1:188460/1‑90 (MQ=255)
ctgcctgcCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAacac < 1:127779/90‑1 (MQ=255)
cgacgaAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTg > 2:163030/1‑90 (MQ=255)
aaTCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGaa > 1:79320/1‑90 (MQ=255)
gACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAagag < 2:643751/90‑1 (MQ=255)
ccgccgCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAggg > 2:572686/1‑90 (MQ=255)
aTTTTGTTGACGCTGGGTATGCAAAAGAATGTGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAgg < 2:148731/90‑1 (MQ=255)
ttgttgACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGt < 2:687856/90‑1 (MQ=255)
gttgACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGa < 1:532446/90‑1 (MQ=255)
ttgACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGaa < 2:305606/90‑1 (MQ=255)
aCGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGGTATTAAGGCGGGAATAc > 1:361948/1‑90 (MQ=255)
tGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAc < 2:315691/90‑1 (MQ=255)
|
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAC > NZ_CP009273/568680‑568838
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ 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
GCGGCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCAT > NZ_CP009273/568655‑568843
|
GCGGCCCCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTA < SRR3722112.312599/100‑1 (MQ=60)
agggtcaaaacccgctattccttgttgcccccgttactttTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAA < SRR3722112.414741/60‑1 (MQ=60)
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGT < SRR3722112.339885/100‑1 (MQ=60)
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGT < SRR3722112.445194/100‑1 (MQ=60)
CCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGT < SRR3722112.616582/100‑1 (MQ=60)
ATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACAC > SRR3722112.190770/1‑100 (MQ=60)
ATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACAC > SRR3722112.190771/1‑100 (MQ=60)
GCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGG < SRR3722112.648113/100‑1 (MQ=60)
CTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTG < SRR3722112.129364/100‑1 (MQ=60)
GCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAA > SRR3722112.80288/1‑100 (MQ=60)
CATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGGTATTAAGGCGGGAATAC > SRR3722112.366585/1‑100 (MQ=60)
TGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGGTATTAAGGCGTGAATACCTACA > SRR3722112.205458/1‑100 (MQ=60)
GTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAG < SRR3722112.540349/100‑1 (MQ=60)
GACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCAT > SRR3722112.323131/1‑100 (MQ=60)
|
GCGGCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCAT > NZ_CP009273/568655‑568843
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
