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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
674,442 |
T→G |
T141P (ACT→CCT) |
ybeT ← |
tetratricopeptide repeat protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 674,442 | 0 | T | G | 93.8%
| 45.7
/ ‑3.2
| 16 | T141P (ACT→CCT) | ybeT | tetratricopeptide repeat protein |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (9/6); total (10/6) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01 |
GTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCT > NZ_CP009273/674355‑674527
|
gttgttTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTGACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGgat > 2:240144/1‑90 (MQ=255)
gttgttTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGgat > 2:519013/1‑90 (MQ=255)
gttgttTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGgat > 1:441395/1‑90 (MQ=255)
tgttTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGatat < 2:504335/90‑1 (MQ=255)
cGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATtgagcat > 1:380786/1‑90 (MQ=255)
ggTCAGTTTTAACCATTTTTGGGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATtgagcat < 1:133121/89‑1 (MQ=255)
ggTCAGTTTTAACCATTTTTGGGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATtgagcat > 2:133121/1‑89 (MQ=255)
ggTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATtgagcatg < 1:66723/90‑1 (MQ=255)
aaCCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCt < 1:68008/90‑1 (MQ=255)
tttttGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTc < 2:305243/90‑1 (MQ=255)
ttAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCag < 1:322848/90‑1 (MQ=255)
tAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCaga > 1:275812/1‑90 (MQ=255)
aaTACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGc > 1:561658/1‑90 (MQ=255)
aaTACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGc > 1:13307/1‑90 (MQ=255)
tGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACg > 2:309777/1‑90 (MQ=255)
tGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACg > 2:37478/1‑90 (MQ=255)
tttCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCg > 2:104489/1‑90 (MQ=255)
aaCCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCa > 2:141088/1‑90 (MQ=255)
aaaGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCt > 1:177852/1‑90 (MQ=255)
|
GTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCT > NZ_CP009273/674355‑674527
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CATTTTTGTAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCTTTGAGGTAGATCC > NZ_CP009273/674343‑674540
|
CATTTTTGTAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGAGCAAAACTAAAGG > SRR3722111.85627/1‑100 (MQ=60)
TTTTTGTAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGAT > SRR3722111.448036/1‑100 (MQ=60)
TGTAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTG < SRR3722111.504048/100‑1 (MQ=60)
GGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCAT > SRR3722111.386250/1‑100 (MQ=60)
CGGTCAGTTTTAACCATTTTTGGGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCC < SRR3722111.134797/100‑1 (MQ=60)
GGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCT < SRR3722111.67514/100‑1 (MQ=60)
AACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTG < SRR3722111.68810/100‑1 (MQ=60)
TCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGA > SRR3722111.279246/1‑100 (MQ=60)
GGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGC > SRR3722111.13461/1‑100 (MQ=60)
GGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGC > SRR3722111.570486/1‑100 (MQ=60)
TTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTT < SRR3722111.327139/100‑1 (MQ=60)
GATCAAACCTAAAGGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCT > SRR3722111.180082/1‑100 (MQ=60)
GGATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCTTTGAGGTAGATCC > SRR3722111.311363/1‑100 (MQ=60)
|
CATTTTTGTAATGTTGTTTGGCGGTCAGTTTTAACCATTTTTGAGATTCATAATGGTTAACATTAATACCTGAGCCATTTCTGTAGATCAAACCTAAAGTATATTGAGCATGAGCATACCCTTGTTCAGCTGCTTCCTTATACCAGAGAATTGCTTTACGGGTGTCGGGTTTGACCCCCAGACCTTTGAGGTAGATCC > NZ_CP009273/674343‑674540
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
