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 |
|
A25 F66 I0 R1
|
20 |
10.5 |
408350 |
90.0% |
367515 |
142.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
461,007 |
T→G |
100% |
I707S (ATC→AGC) |
lon → |
Lon protease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 461,007 | 0 | T | G | 85.1%
| 29.7
/ ‑2.6
| 16 | I707S (ATC→AGC) | lon | Lon protease |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base G (6/7); total (7/9) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTGACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAT‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAA > NC_000913/460872‑461141
|
gTGACACCCACGTCCACGTCCCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTg < 1:129586/143‑1 (MQ=255)
acgtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCCCCGCGCTGGTTTCTTGCCTGACCGGTAACCCGCTTCGTGCCGAAGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAg < 1:128476/143‑1 (MQ=255)
acgtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAg < 2:186807/143‑1 (MQ=255)
gtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCCATGACCGGTGCGAG‑CTCTCTGCGTGGTCAGGt > 1:184187/1‑143 (MQ=255)
gacgtACCGGAGGGTGGGACGGCGAGTGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTGCTTGCCTGACCGGTAACGCGGTTCGTGCCGATGTGGCAATGACAGGTGAGAG‑CACTCTGCGTGGTGAGGTACt < 2:43629/142‑1 (MQ=255)
cccGGAAGGGGCGACGCCGAGCGATGGTCCGAGTGCCGGTATTGCTATGTGCCCCGCGCTGGTTTCTTGCCTGACCGGTACCCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGa < 2:149730/142‑1 (MQ=255)
ggTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACGGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CCCTCTGCGTGGTCAGGTTCTGCCGATCggtgg > 1:139582/1‑143 (MQ=255)
gTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGCTGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGGTTGAAAGAAAAACTGCTGGCAGCGCATcgc > 2:74624/1‑143 (MQ=255)
gCACCGCGCCGGCTTCGTGCCTCACCGCGAACCCGGTGCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTaaa < 1:60677/143‑1 (MQ=255)
cgCCGGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCTATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGtt < 1:194711/142‑1 (MQ=255)
aCCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAT‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAACCAGTGCTAATTCCGTTCGaaaa > 1:128907/1‑143 (MQ=255)
aCCCGTTGCGTGCCGATGTCGCAATGACCGGTGAGAT‑CACTCTGCGTGGTCAGCTACTGCCGATCGGTGGTTTGAACGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACTGTGCTAATTCCGTTCGAAAATAAAcgc < 2:16302/143‑1 (MQ=255)
cGGTTCGTGCCGATGTGGCAATGACCGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGTGCATCGCGGCGGGCGTAAAACAGGGCTAATTCCGCTCGACAATAAACGCGac > 2:190919/1‑142 (MQ=255)
gaggcGAGGTGTCAATGACTCGTG‑GATGCACACTGCGTGGTCAGCTACTGCCGATCGGTGGTTAGAAAGAAAAACGCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGaa < 2:8695/139‑1 (MQ=255)
cGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGGTCCGGAAGAGATTCCTGACAACgaca > 2:30442/1‑140 (MQ=255)
cGGTGAGAG‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGAACTGGAAGAGATTCCTGCAAACGTaa > 2:19513/1‑143 (MQ=255)
|
GTGACATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAT‑CACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAA > NC_000913/460872‑461141
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
