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 |
1,021,663 |
(A)5→4 |
coding (1737/2055 nt) |
helD → |
DNA helicase IV |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,021,659 | 0 | A | . | 90.9%
| 69.6
/ 4.3
| 22 | coding (1733/2055 nt) | helD | DNA helicase IV |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base . (10/10); total (12/10) |
| Fisher's exact test for biased strand distribution p-value = 4.81e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021571‑1021744
|
ttGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGaa > 1:820428/1‑90 (MQ=255)
tAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCa < 2:158966/90‑1 (MQ=255)
aGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAac > 1:67304/1‑90 (MQ=255)
aGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAac < 1:688176/90‑1 (MQ=255)
aGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAac > 1:704275/1‑90 (MQ=255)
tctGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGc > 2:405417/1‑90 (MQ=255)
tctGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGc > 2:553688/1‑90 (MQ=255)
tctGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCt > 1:730105/1‑90 (MQ=255)
tATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGa > 2:787979/1‑90 (MQ=255)
tGCCAAACCGGAAGAGCGCATTCTGATCCTGGTGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAg < 1:756322/90‑1 (MQ=255)
aaCCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCa > 2:697063/1‑90 (MQ=255)
gcATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTAt > 1:704916/1‑90 (MQ=255)
ttCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc < 2:45047/90‑1 (MQ=255)
aTCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑GAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTc < 2:223770/90‑1 (MQ=255)
ccTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCAt > 2:751648/1‑90 (MQ=255)
ccTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCAt < 2:820428/90‑1 (MQ=255)
ttACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCaaa > 1:257813/1‑90 (MQ=255)
aTCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCa < 1:209103/90‑1 (MQ=255)
cacaTGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAAc < 1:761584/90‑1 (MQ=255)
aTGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAgg > 1:44629/1‑90 (MQ=255)
tGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGc < 1:287154/90‑1 (MQ=255)
tGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTAc > 2:147713/1‑90 (MQ=255)
ccTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGtcatc < 1:356090/90‑1 (MQ=255)
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021571‑1021744
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCTTGCAGGAG > NZ_CP009273/1021571‑1021762
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAAC > SRR3722079.67857/1‑100 (MQ=60)
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAAC > SRR3722079.711744/1‑100 (MQ=60)
GGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCT > SRR3722079.737910/1‑100 (MQ=60)
AGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCG < SRR3722079.695408/100‑1 (MQ=60)
TGCCAAACCGGAAGAGCGCATTCTGATCCTGGTGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCG < SRR3722079.764410/100‑1 (MQ=60)
CCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTAT > SRR3722079.712396/1‑100 (MQ=60)
TCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAA > SRR3722079.259979/1‑100 (MQ=60)
TTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGG > SRR3722079.44969/1‑100 (MQ=60)
ATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGAT < SRR3722079.210895/100‑1 (MQ=60)
CACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTA < SRR3722079.769731/100‑1 (MQ=60)
TGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTC < SRR3722079.289532/100‑1 (MQ=60)
CCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT < SRR3722079.358882/100‑1 (MQ=60)
AGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCTTGCAGGAG < SRR3722079.559007/100‑1 (MQ=60)
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCTTGCAGGAG > NZ_CP009273/1021571‑1021762
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
