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 |
|
A6 F1 I2 R1
|
67 |
27.9 |
1239648 |
95.3% |
1181384 |
112.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,993,464 |
Δ1 bp |
coding (2312/2547 nt) |
cyaA → |
adenylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,993,464 | 0 | A | . | 89.7%
| 90.7
/ 8.8
| 30 | coding (2312/2547 nt) | cyaA | adenylate cyclase |
| Reads supporting (aligned to +/- strand): ref base A (0/3); new base . (13/13); total (13/17) |
| Fisher's exact test for biased strand distribution p-value = 2.32e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01 |
ATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCAGATTGTGA > NC_000913/3993326‑3993589
|
aTCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTGTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATcacca > 1:370416/1‑139 (MQ=255)
ttGCCTGCTAAGGGATCATCCTGTTCTTTTTCGAAGAAACGCAAGACGAGATTGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGAc < 1:611913/139‑1 (MQ=255)
tGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACg > 1:399454/1‑139 (MQ=255)
gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCg > 2:97582/1‑139 (MQ=255)
gAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCg < 2:399454/139‑1 (MQ=255)
taatcctattCTTTCACGAAGAAACACAAGACGAGAATGGCTTTAATATCTACATTCGCGACGAAAGCAACCGGGTAGAGGTAAATCACC‑CTGCGAAGGCAGCAAAGACGAGCTAGTACGTGACGGCAGTCGCTTCTAc < 1:220942/131‑1 (MQ=255)
ccAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGt < 1:504690/139‑1 (MQ=255)
aGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGTAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCa < 2:421122/139‑1 (MQ=255)
ttCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATc > 1:516893/1‑139 (MQ=255)
ttCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATg < 2:370416/139‑1 (MQ=255)
tCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGa < 2:394023/139‑1 (MQ=255)
aCGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAgg < 1:293813/76‑1 (MQ=255)
aCGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAgg > 2:293813/1‑76 (MQ=255)
cAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCt < 2:208620/139‑1 (MQ=255)
cAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTa < 1:346530/139‑1 (MQ=255)
gACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACgg > 1:516162/1‑139 (MQ=255)
cGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCt > 1:157375/1‑139 (MQ=255)
aaTGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAg > 1:488446/1‑139 (MQ=255)
cTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGa < 1:22724/113‑1 (MQ=255)
cTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGa > 2:22724/1‑113 (MQ=255)
cTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGt < 2:352023/81‑1 (MQ=255)
cTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGt > 1:352023/1‑81 (MQ=255)
cTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCa > 2:494978/1‑139 (MQ=255)
cTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCa > 2:575656/1‑139 (MQ=255)
tcGACGAATGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCg > 2:400053/1‑139 (MQ=255)
acgaAAGCAACCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCTAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAg < 1:400053/139‑1 (MQ=255)
aaCCGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCa < 1:494978/139‑1 (MQ=255)
ccGGGTTGAGGTATATCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCAGa < 2:516893/139‑1 (MQ=255)
tGAGGTAAATC‑CCCCTGCGAAGGCAGCAAAGAAGAGCTGGTACGGTACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCAGATTGTGa < 2:563064/139‑1 (MQ=255)
tatCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCa > 1:459745/1‑89 (MQ=255)
tatCACC‑CTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCa < 2:459745/89‑1 (MQ=255)
|
ATCACGTCAAATTACCGGCGGTGGTGGACGGCTTTGCCAGCGAAGGGATCATCCAGTTCTTTTTCGAAGAAACGCAAGACGAGAATGGCTTTAATATCTACATTCTCGACGAAAGCAACCGGGTTGAGGTATATCACCACTGCGAAGGCAGCAAAGAGGAGCTGGTACGTGACGTCAGTCGCTTCTACTCGTCATCGCATGACCGTTTTACCTACGGCTCAAGCTTCATCAACTTCAACCTGCCGCAGTTCTATCAGATTGTGA > NC_000913/3993326‑3993589
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
