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 |
|
A2 F5 I178 R1
|
167 |
28.0 |
1137820 |
95.3% |
1084342 |
115.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
446,387 |
T→C |
D227G (GAT→GGT) |
cyoA ← |
cytochrome o ubiquinol oxidase subunit II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 446,387 | 0 | T | C | 94.7%
| 55.9
/ ‑5.6
| 19 | D227G (GAT→GGT) | cyoA | cytochrome o ubiquinol oxidase subunit II |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (8/10); minor base G (0/1); total (8/11) |
| 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 |
GTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGATCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAAT > NZ_CP009273/446251‑446520
|
gTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGAccc < 1:3237/139‑1 (MQ=255)
gTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGAccc < 1:49884/139‑1 (MQ=255)
gTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCgg < 1:450023/136‑1 (MQ=255)
aCGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCaa < 1:522332/139‑1 (MQ=255)
gaAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTg < 1:454313/139‑1 (MQ=255)
gcgcGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCt < 1:71504/139‑1 (MQ=255)
ggTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCaa > 1:104372/1‑65 (MQ=255)
ggTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCaa < 2:104372/65‑1 (MQ=255)
ggTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCg < 2:521748/95‑1 (MQ=255)
ggTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCg > 1:521748/1‑95 (MQ=255)
gtgtTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGt > 2:66648/1‑139 (MQ=255)
tgtTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCaa < 2:235361/63‑1 (MQ=255)
tgtTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCaa > 1:235361/1‑63 (MQ=255)
tgtTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGtt > 2:160718/1‑139 (MQ=255)
tgtTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGtt > 2:176071/1‑139 (MQ=255)
ttCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTgg < 1:160718/139‑1 (MQ=255)
gCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAgg < 1:66648/138‑1 (MQ=255)
ttcGACGCACTGGTCAAATGCGGCGCGAGCCGGTGTTGCAATAGCTTTGAACATCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATGCCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGt < 2:410808/136‑1 (MQ=255)
tCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCa < 1:343881/139‑1 (MQ=255)
cgcgACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAAt > 1:469821/1‑139 (MQ=255)
cgcgACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAAt > 1:79288/1‑139 (MQ=255)
|
GTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGATCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAAT > NZ_CP009273/446251‑446520
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
ACAAGTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGATCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAATC > NZ_CP009273/446247‑446521
|
ttttttttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctctgagatgtgtataagagacagTGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTG < SRR3722132.8135/72‑1 (MQ=60)
AGTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAAT < SRR3722132.3301/151‑1 (MQ=60)
AGTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAAT < SRR3722132.50767/151‑1 (MQ=60)
GGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAG < SRR3722132.458113/148‑1 (MQ=60)
CACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAAC < SRR3722132.531577/151‑1 (MQ=60)
AGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCC < SRR3722132.462477/151‑1 (MQ=60)
GGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGG < SRR3722132.72802/151‑1 (MQ=60)
ATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgct > SRR3722132.106320/1‑87 (MQ=60)
ATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGtctcttatacacatctccgagcccacgagac > SRR3722132.530987/1‑120 (MQ=60)
GTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttg > SRR3722132.239775/1‑85 (MQ=60)
GTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGC < SRR3722132.163716/151‑1 (MQ=60)
CGCTTTTGCGACCCACTGGTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCAT < SRR3722132.67868/150‑1 (MQ=60)
GTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAATC < SRR3722132.350264/151‑1 (MQ=60)
GTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAATC > SRR3722132.478226/1‑151 (MQ=60)
GTCGAATGCGGCGCGACCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAATC > SRR3722132.80724/1‑151 (MQ=60)
|
ACAAGTCTGGTTTCACGTTGGAGAAATATTCCACCTGGTTGTATTCGCTAGGCGCGGCCAGTTTTTCGAACGCAGCCATGTCAGACATGGTGTTCGGCGACTGCTTCGCTTTTGCGACCCACTGGTCGAATGCGGCGCGATCCGGTGTTGCAATAGCTTTGAACTTCATGCCTGAGAAGCCCGGGCCGCTGTAGCTGGCGGAGATACCGTCATAAGTGCCGGGTTCGTTGGCGATCAGATGCAGGCGAGTCTGCATACCGGCCATGGCATAAATC > NZ_CP009273/446247‑446521
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
