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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,065,426 |
T→G |
T129P (ACC→CCC) |
rutF ← |
pyrimidine utilization flavin reductase protein F |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,065,426 | 0 | T | G | 96.0%
| 76.2
/ NA
| 25 | T129P (ACC→CCC) | rutF | pyrimidine utilization flavin reductase protein F |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (15/9); total (16/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACC > NZ_CP009273/1065347‑1065502
|
cTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTc < 1:103673/90‑1 (MQ=255)
tCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCaccacc < 2:566575/90‑1 (MQ=255)
tCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCaccacc < 1:249206/90‑1 (MQ=255)
tCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCaccacc < 2:469273/90‑1 (MQ=255)
tCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCaccacc < 1:346461/90‑1 (MQ=255)
gTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTc > 1:683979/1‑90 (MQ=255)
gTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTc > 2:292952/1‑90 (MQ=255)
tAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCa > 2:816127/1‑90 (MQ=255)
ggtgtggtgtGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAAc < 1:438464/90‑1 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTc > 2:810143/1‑60 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTc < 1:810143/60‑1 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGaa > 2:708087/1‑90 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGaa > 2:461769/1‑90 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGaa > 1:333779/1‑90 (MQ=255)
gtggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGaa > 2:563640/1‑90 (MQ=255)
gtggtgggACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGGCAAACGaa > 2:610253/1‑90 (MQ=255)
ggtgtgACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAAc > 2:97535/1‑90 (MQ=255)
gACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCagag > 2:503357/1‑90 (MQ=255)
gACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCagag > 2:783963/1‑90 (MQ=255)
gACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCagag > 1:536506/1‑90 (MQ=255)
aCGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGc < 1:15521/90‑1 (MQ=255)
gAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCtt > 1:135457/1‑90 (MQ=255)
ttCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTg > 2:521086/1‑90 (MQ=255)
gcgcAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCAt > 1:777365/1‑90 (MQ=255)
aGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCAcc < 2:95104/90‑1 (MQ=255)
|
CTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACC > NZ_CP009273/1065347‑1065502
|
| 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
CTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGCG > NZ_CP009273/1065347‑1065520
|
gagatgtgtataagagaCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGC < SRR3722079.818832/83‑1 (MQ=60)
CTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGC < SRR3722079.104501/100‑1 (MQ=60)
TCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATAC < SRR3722079.251294/100‑1 (MQ=60)
TCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATAC < SRR3722079.349201/100‑1 (MQ=60)
ACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTC > SRR3722079.691170/1‑100 (MQ=60)
CCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAA > SRR3722079.336430/1‑100 (MQ=60)
GGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAG < SRR3722079.442269/100‑1 (MQ=60)
GGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAG > SRR3722079.541544/1‑100 (MQ=60)
GTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTT > SRR3722079.136601/1‑100 (MQ=60)
ACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGT < SRR3722079.15630/100‑1 (MQ=60)
CGCTTCGATGGCGCAAAACAGAATGTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCAT > SRR3722079.785695/1‑100 (MQ=60)
GTCGTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGG > SRR3722079.228667/1‑100 (MQ=60)
GTGGGGGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGCG > SRR3722079.330212/1‑100 (MQ=60)
|
CTGCGATCGAACCACACCAGCCCGTAGGGTGTGGTGTGACGATGAATCGCTTCGATGGCGCAAAACAGAATGTCGTGGGTGCCGACGCTCACCACCTGGCTGATACGGCAGTCAAACGAAACCAGAGCCTCTTCCAGTTGCGGGCATCCGGTCACCCCCGTCTGCCAGCGGGCG > NZ_CP009273/1065347‑1065520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
