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 I197 R1
|
189 |
12.7 |
697584 |
97.1% |
677354 |
86.2 |
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 | 80.0%
| 22.3
/ 3.2
| 15 | G71G (GGA→GGG) | ybcO | DUF1364 domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (1/2); new base G (5/7); total (6/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.75e-01 |
GCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGT > NZ_CP009273/568674‑568828
|
gCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGa > 1:112015/1‑90 (MQ=255)
cccgACCTGATTGCCACCATTGCATGGTTTGCCTGCCCCGACGAAATCGACCCCCCCACCCCTTTTGTTTAACGTGGGGATGCAAAAGaa > 1:198662/4‑90 (MQ=255)
tGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGa < 2:197349/90‑1 (MQ=255)
ccaTTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTa < 2:311331/90‑1 (MQ=255)
aTGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCgag < 1:282149/90‑1 (MQ=255)
ctgcctgcCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAacac < 1:217435/90‑1 (MQ=255)
tgcctgccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAAcaca > 1:104022/1‑90 (MQ=255)
gcctgccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAg > 1:174270/1‑90 (MQ=255)
tgccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGtt > 2:103673/1‑90 (MQ=255)
ccACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTAt > 2:110923/1‑90 (MQ=255)
cACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATc < 2:198662/90‑1 (MQ=255)
gACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAagag < 1:245908/90‑1 (MQ=255)
gACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAagag < 1:344653/90‑1 (MQ=255)
cgcaTTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGttatta < 1:306354/90‑1 (MQ=255)
ttgttgACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGt < 1:110923/90‑1 (MQ=255)
|
GCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGT > NZ_CP009273/568674‑568828
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 29 ≤ 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
GTGCGGCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCA > NZ_CP009273/568653‑568845
|
GTGCGGCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGG > SRR3722076.258514/1‑100 (MQ=60)
CCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAA < SRR3722076.108776/100‑1 (MQ=60)
GTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGA > SRR3722076.113367/1‑100 (MQ=60)
tcctcccattggatgtccgGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCG < SRR3722076.276895/81‑1 (MQ=60)
tccatccacgacatgtgaTGCCTTCCACGCCGAAAACGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAACAGAATGCGCGCTGGAAGGTATGGCG < SRR3722076.192563/82‑1 (MQ=60)
TTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACA > SRR3722076.105282/1‑100 (MQ=60)
TGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAG > SRR3722076.176465/1‑100 (MQ=60)
ATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTT < SRR3722076.286342/100‑1 (MQ=60)
CTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTG < SRR3722076.220361/100‑1 (MQ=60)
GACCGCCGCACGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTA < SRR3722076.249407/100‑1 (MQ=60)
GACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTA < SRR3722076.349904/100‑1 (MQ=60)
CGCATTTTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAAT < SRR3722076.310964/100‑1 (MQ=60)
TTGTTGACGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTAC < SRR3722076.112268/100‑1 (MQ=60)
CGCTGGGTATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCA > SRR3722076.156961/1‑100 (MQ=60)
|
GTGCGGCACCGGTACGAAACCGCCAGACCTGATTGCCACCATTGCATGTTCTGCCTGCCACGACGAAATCGACCGCCGCACGCATTTTGTTGACGCTGGATATGCAAAAGAATGCGCGCTGGAAGGTATGGCGAGAACACAGGTTATCTGGCTGAAAGAGGGGGTTATTAAGGCGTGAATACCTACAGCATCA > NZ_CP009273/568653‑568845
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
