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 |
|
A5 F1 I1 R1
|
770 |
51.4 |
2439994 |
93.8% |
2288714 |
110.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,185,875 |
(G)7→8 |
intergenic (‑79/‑42) |
rcnR ← / → rcnA |
transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,185,868 | 1 | . | G | 80.0%
| 45.6
/ 7.2
| 20 | intergenic (‑72/‑49) | rcnR/rcnA | transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base G (11/5); total (12/8) |
| Fisher's exact test for biased strand distribution p-value = 2.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.99e-01 |
TGGCCCTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCAT > NC_000913/2185735‑2185997
|
tGGCCTTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAATACCTGGTTAACAAGAATATAAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTATT‑ggg‑g‑g < 1:64322/139‑1 (MQ=255)
tgCCCTGAATGTTTCTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGAAATGGCAACACCTGGTTAACAAGAAAATTAAAAATCATAGCACTATTAATCGGCTGGGGGGTAGTATCAGGTACT‑ggg‑g‑g‑g < 1:117269/138‑1 (MQ=255)
cttcagcTTAGTGGCACGTGCTTTCAGTTTCTGTTTATCACGGTTTGAATGAGTCATAGGAATACCTGGTTAACAAAAATAAGAAAGATCATAGCACTATTAATCTTCGGGGGGGTAGTATCAGGTACT‑ggg‑g‑g‑gggag < 2:463327/133‑4 (MQ=255)
cACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTTATCTACTGGTGGGTAGTATCAGGTACT‑GGG‑G‑G‑GGAGTAGAATCAGATTGcc < 1:750667/139‑1 (MQ=255)
tttaGTTTTTTTTTATAACGGAGTGTATGACACATGGCAACTCCTTGTTAACAAAAATATGAAAAATCATAGCATTATTAATCGACTGGGGGGTAGTATCAAGTAATGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTaa < 1:384742/136‑1 (MQ=255)
aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAGTCTACTGGGGGGTAGTATCAGGTACT‑ggg‑g‑g‑gggag < 1:332745/84‑4 (MQ=255)
aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACaa > 2:528443/1‑139 (MQ=255)
aTGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑ggg‑g‑g‑gggag > 2:332745/1‑81 (MQ=255)
ggCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGGTGGAACAAATTTGCGAATTTAAACTAAAAAATATTATTATGAACGGAATTAACact > 2:840364/1‑137 (MQ=255)
cTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCa > 2:1205597/1‑139 (MQ=255)
cAAGAATATGAAAAAGCATAGCACTATTAATCCACTGGGCGGTAGTATCAGGTACT‑GGG‑G‑GCGGAGTAGACTCAGTATGCCGAAGTAATACTATGAATTACTATCATG‑ACCGAATTTACAACTCTACTGCAGCAAGGaa > 1:184797/1‑139 (MQ=255)
attagagacaggcTACTGGGTGTTAGTATAAGTTCCTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATccc < 1:269173/127‑1 (MQ=255)
tataAAACTACTGGGGGGTAGAAAGAAGTACT‑GGGAG‑G‑AGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAgcg < 1:528443/139‑1 (MQ=255)
cTACTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGc > 1:945638/1‑112 (MQ=255)
cTACTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGc < 2:945638/112‑1 (MQ=255)
cTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGCGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACt > 2:516379/1‑139 (MQ=255)
cTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTaa > 2:1121085/1‑60 (MQ=255)
cTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTaa < 1:1121085/60‑1 (MQ=255)
cTGGGGGGTAGTATCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACt > 1:750499/1‑139 (MQ=255)
gtagtaTCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCtctgtctcttat > 2:269173/1‑128 (MQ=255)
tagtaTCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAActc > 2:415431/1‑82 (MQ=255)
tagtaTCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAActc < 1:415431/82‑1 (MQ=255)
gtaTCAGGTACTGGGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCtt > 2:839577/1‑139 (MQ=255)
tCAGGTACTGGGG‑G‑G‑GGAGGAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGGATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTAATTGGTGCGCTTCAt > 1:1117006/1‑139 (MQ=255)
tCAGATACT‑GGG‑GAG‑GAAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCAt < 2:750499/139‑1 (MQ=255)
|
TGGCCCTGAATCTTACTGGCACGCGCTTTCAGTTTCTGTTTATCACGGATTGTATGAGACATGGCAACACCTGGTTAACAAGAATATGAAAAATCATAGCACTATTAATCTACTGGGGGGTAGTATCAGGTACT‑GGG‑G‑G‑GGAGTAGAATCAGATTGCCGAATTAATACTAAGAATTATTATCATG‑ACCGAATTTACAACTCTTCTTCAGCAAGGAAACGCCTGGTTCTTCATCCCCAGCGCCATCTTACTTGGTGCGCTTCAT > NC_000913/2185735‑2185997
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
