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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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 | . | 100.0%
| 50.4
/ NA
| 13 | coding (1733/2055 nt) | helD | DNA helicase IV |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (7/6); total (7/6) |
CTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021583‑1021744
|
ctctctGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAacac > 1:514460/1‑90 (MQ=255)
gcATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTAt > 2:507560/1‑90 (MQ=255)
ttCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc < 2:522235/90‑1 (MQ=255)
tGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGc > 1:552108/1‑90 (MQ=255)
ggCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc > 1:459848/1‑80 (MQ=255)
ggCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc < 2:459848/80‑1 (MQ=255)
gcgcGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCa > 1:108910/1‑90 (MQ=255)
tGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGc < 1:222786/90‑1 (MQ=255)
cTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTa > 1:288467/1‑90 (MQ=255)
tGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTAc < 2:552108/90‑1 (MQ=255)
gCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACg > 1:148148/1‑90 (MQ=255)
ccAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGt < 2:108910/90‑1 (MQ=255)
ccTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGtcatc < 1:507560/90‑1 (MQ=255)
|
CTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021583‑1021744
|
| 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
GCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT > NZ_CP009273/1021573‑1021754
|
GCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACAC > SRR3722092.524771/1‑100 (MQ=60)
ATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGC > SRR3722092.563190/1‑100 (MQ=60)
TTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCC > SRR3722092.468930/1‑100 (MQ=60)
TCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCA > SRR3722092.110765/1‑100 (MQ=60)
CACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTA > SRR3722092.293455/1‑100 (MQ=60)
CATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACG > SRR3722092.150642/1‑100 (MQ=60)
TGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTC < SRR3722092.226426/100‑1 (MQ=60)
gacaggcctggAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCG < SRR3722092.1387/89‑1 (MQ=60)
CCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT < SRR3722092.517715/100‑1 (MQ=60)
|
GCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT > NZ_CP009273/1021573‑1021754
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
