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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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%
| 101.7
/ NA
| 24 | coding (1733/2055 nt) | helD | DNA helicase IV |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (13/11); total (13/11) |
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021571‑1021744
|
ttGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGaa > 1:757782/1‑90 (MQ=255)
aGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAac > 1:226988/1‑90 (MQ=255)
gTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGcc < 1:558/90‑1 (MQ=255)
cAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTg > 2:454087/1‑90 (MQ=255)
aaCCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCa > 1:154169/1‑90 (MQ=255)
aaCCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCa > 1:794174/1‑90 (MQ=255)
ggAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGaaaagc > 1:1153743/1‑60 (MQ=255)
ggAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGaaaagc < 2:1153743/62‑3 (MQ=255)
aaGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGa < 2:1180101/90‑1 (MQ=255)
ttCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc > 1:1086668/1‑90 (MQ=255)
ttCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAc > 1:1071026/1‑90 (MQ=255)
gATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATAACCAtt > 1:940564/1‑90 (MQ=255)
aTCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGTTGGCCGAAGTTGCAAATCGACTTTATGACCATTc < 2:794174/90‑1 (MQ=255)
ccTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCAt < 1:87701/90‑1 (MQ=255)
cgTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCa > 1:861713/1‑90 (MQ=255)
gTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCaa < 1:705385/90‑1 (MQ=255)
aTCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCa < 2:154169/90‑1 (MQ=255)
aTGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTc < 2:1123538/69‑1 (MQ=255)
aTGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTc > 1:1123538/1‑69 (MQ=255)
tGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGc < 2:1071026/90‑1 (MQ=255)
tGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGc < 2:226811/90‑1 (MQ=255)
gAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCg > 2:112837/1‑90 (MQ=255)
ccTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGAtt < 1:1162836/90‑1 (MQ=255)
cTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTa > 2:890503/1‑90 (MQ=255)
tGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTAc > 1:200098/1‑90 (MQ=255)
aGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGtca > 2:998479/1‑90 (MQ=255)
ccTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGtcatc < 1:77298/90‑1 (MQ=255)
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATC > NZ_CP009273/1021571‑1021744
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ 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
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT > NZ_CP009273/1021571‑1021754
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAAC > SRR3722089.229873/1‑100 (MQ=60)
GGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCA > SRR3722089.805116/1‑100 (MQ=60)
GGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCA > SRR3722089.156081/1‑100 (MQ=60)
GTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAA < SRR3722089.563/100‑1 (MQ=60)
ATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCctgtctcttatacacatc > SRR3722089.1171300/1‑82 (MQ=60)
GAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAC > SRR3722089.1103041/1‑100 (MQ=60)
GAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGAC > SRR3722089.1087109/1‑100 (MQ=60)
AGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATAACCATT > SRR3722089.954338/1‑100 (MQ=60)
GATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCA > SRR3722089.874038/1‑100 (MQ=60)
CCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAG < SRR3722089.88781/100‑1 (MQ=60)
GTTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAG < SRR3722089.714577/100‑1 (MQ=60)
TTACCATCACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAActgtctcttat > SRR3722089.1140587/1‑89 (MQ=60)
ACATGAGGCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTAC > SRR3722089.202622/1‑100 (MQ=60)
GCCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCA > SRR3722089.158119/1‑100 (MQ=60)
CCTGCCAGCCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCAT < SRR3722089.1180519/100‑1 (MQ=60)
CCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT > SRR3722089.441115/1‑100 (MQ=60)
CCTGG‑AAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT < SRR3722089.78241/100‑1 (MQ=60)
|
TTGCTGGATAAGCTCTCTGGTTATGCCAAACCGGAAGAGCGCATTCTGATCCTGGCGCGTTACCATCACATGAGGCCTGCCAGCCTGGAAAAAGCGGCAACACGCTGGCCGAAGTTGCAAATCGACTTTATGACCATTCATGCCAGCAAAGGGCAACAGGCGGATTACGTCATCATCGTTGGCT > NZ_CP009273/1021571‑1021754
|
| 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: ‑ |
