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 |
|
A10 F1 I2 R1
|
757 |
38.1 |
1607544 |
96.5% |
1551279 |
117.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,535,612 |
(GA)4→5 |
coding (257/1353 nt) |
envZ ← |
sensory histidine kinase in two‑component regulatory system with OmpR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,535,603 | 1 | . | A | 90.0%
| 83.9
/ 3.8
| 30 | coding (266/1353 nt) | envZ | sensory histidine kinase in two‑component regulatory system with OmpR |
| Reads supporting (aligned to +/- strand): ref base . (0/3); new base A (15/12); total (15/15) |
| Fisher's exact test for biased strand distribution p-value = 2.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
| * | NC_000913 | 3,535,603 | 2 | . | G | 90.0%
| 96.5
/ 3.9
| 30 | coding (266/1353 nt) | envZ | sensory histidine kinase in two‑component regulatory system with OmpR |
| Reads supporting (aligned to +/- strand): ref base . (0/3); new base G (15/12); total (15/15) |
| Fisher's exact test for biased strand distribution p-value = 2.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
GAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGT‑‑AGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTA > NC_000913/3535480‑3535728
||
gAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGT‑‑Agagagagagatccc < 2:168568/139‑7 (MQ=255)
gAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGT‑‑Agagagagagatccc < 1:791392/139‑7 (MQ=255)
cTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGT‑‑Agagagagagatccccag < 2:139248/139‑10 (MQ=255)
cTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGa > 1:470262/1‑139 (MQ=255)
cgcgCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTcc > 1:467814/1‑139 (MQ=255)
ccgccCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAgg > 1:726098/1‑139 (MQ=255)
gcgcCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGc > 1:351259/1‑139 (MQ=255)
ccATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTg < 1:494336/139‑1 (MQ=255)
tCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGttt > 2:198744/1‑139 (MQ=255)
aGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCg < 1:198744/139‑1 (MQ=255)
gtTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtc > 1:8019/1‑139 (MQ=255)
tGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtcat < 1:695014/139‑1 (MQ=255)
gcgcCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtcatc < 1:19667/139‑1 (MQ=255)
gcgcCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtcatc < 2:726098/139‑1 (MQ=255)
gcgcCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGtcatc > 2:19667/1‑139 (MQ=255)
aaCGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATa > 1:156830/1‑139 (MQ=255)
cGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGcaca < 1:463567/89‑1 (MQ=255)
cGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGcaca > 2:463567/1‑89 (MQ=255)
cGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACg > 2:86232/1‑139 (MQ=255)
aCCTGCCTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACtt < 2:467814/139‑1 (MQ=255)
ccTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTAc > 1:352691/1‑139 (MQ=255)
ccTCTTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTAc > 2:203915/1‑139 (MQ=255)
ctTCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTAcgcg < 2:444224/139‑1 (MQ=255)
tCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTAcgc < 1:643360/136‑1 (MQ=255)
tCGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTAcgc > 2:643360/1‑136 (MQ=255)
cGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCa < 1:394074/95‑1 (MQ=255)
cGGCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCa > 2:394074/1‑95 (MQ=255)
ggCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGa > 2:320356/1‑139 (MQ=255)
ggCAGCCTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGa < 2:470262/139‑1 (MQ=255)
ccTCGTTGGAGTAGAGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTtta < 1:320356/139‑1 (MQ=255)
||
GAACTTTTGTTGACCTCAACGCGCACTTCCGTCGGGCCGCCCAGTTGCTGCGCCATCTGATGGCTTAAGAATTCATAGTGTTGCGCCCAACGCAGACCTGCCTCTTCGGCAGCCTCGTTGGAGT‑‑AGAGAGAGATCCCCAGCTCACGGTAGATCTCCCGACGGAAAGCGGGAGGCACAACCAACTGCGTGCCGTCCTCCAGTTGCAGTTTGTCGGTCATCAACATACGCACTTCGTACGCGAGGACTTTA > NC_000913/3535480‑3535728
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
