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 |
|
A8 F1 I2 R1
|
97 |
53.3 |
2484976 |
94.5% |
2348302 |
111.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,380,360 |
(C)5→6 |
coding (284/1296 nt) |
menF ← |
isochorismate synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,380,355 | 1 | . | C | 96.8%
| 108.6
/ ‑3.0
| 31 | coding (289/1296 nt) | menF | isochorismate synthase 2 |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (14/16); total (14/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01 |
ATTCTTTTGCCTGAATCGCATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAG‑CCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCATTACGTTGTTGCCAGTAGAAT > NC_000913/2380217‑2380488
|
aTTCTTTTGCCTGAATCGCATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAg < 2:316233/139‑1 (MQ=255)
gCCTGAATCGCATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCGGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAG‑CCCCCcaa < 2:278088/139‑1 (MQ=255)
gCCTGAATCGCATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAG‑ccccccaa < 1:271544/139‑4 (MQ=255)
cATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGt > 1:301988/1‑139 (MQ=255)
gCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTg < 1:884732/139‑1 (MQ=255)
ttCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTg < 1:1108192/139‑1 (MQ=255)
aTAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCgaagaa > 2:258606/1‑139 (MQ=255)
tAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGaaa < 1:498389/139‑1 (MQ=255)
cGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACg < 1:655962/139‑1 (MQ=255)
cGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACg > 2:655962/1‑139 (MQ=255)
gTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGt > 1:1123279/1‑139 (MQ=255)
tCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGtt < 2:1123279/139‑1 (MQ=255)
gCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAg > 2:684720/1‑102 (MQ=255)
gCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAg < 1:684720/102‑1 (MQ=255)
ccGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGc < 2:478201/139‑1 (MQ=255)
aGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTgg > 1:80008/1‑139 (MQ=255)
ggCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCaa < 1:154126/139‑1 (MQ=255)
ccGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGc < 1:376041/90‑1 (MQ=255)
ccGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGc > 2:376041/1‑90 (MQ=255)
ccGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTa > 1:1004398/1‑139 (MQ=255)
cAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAg < 1:258606/139‑1 (MQ=255)
ggggTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAg > 1:943504/1‑43 (MQ=255)
ggggTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAg < 2:943504/43‑1 (MQ=255)
gTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATc > 2:1229672/1‑123 (MQ=255)
gTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATc < 1:1229672/123‑1 (MQ=255)
tAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGc < 2:49427/139‑1 (MQ=255)
aaTTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCga < 1:161781/72‑1 (MQ=255)
aaTTGCCCTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCga > 2:161781/1‑72 (MQ=255)
cccTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCa > 2:1046089/1‑139 (MQ=255)
cTGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCAtt < 2:88683/139‑1 (MQ=255)
tGCGACGGGTCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCATTa > 1:582632/1‑139 (MQ=255)
tCAAAAGCATTCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCATTACGTTGTTGc < 2:1004398/139‑1 (MQ=255)
ttCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCATTACGTTGTTGCCAGTAGAAt > 1:314732/1‑139 (MQ=255)
ttCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGATAATCGCGCCCAGGACGACAGCTTCTtcatca < 1:832983/115‑1 (MQ=255)
ttCAGCCCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGATAATCGCGCCCAGGACGACAGCTTCTtcatca > 2:832983/1‑115 (MQ=255)
|
ATTCTTTTGCCTGAATCGCATCGTGCTGAAGGGAGCTTTCGCTGAATAGCGTCAGCCGCAGCGTGGCTTTACCGCCACAGCGTCGCCATTCCAGGCGGGGTAAAAGTAAATTGCCCTGCGACGGGTCAAAAGCATTCAG‑CCCCCAAATGCGTAAGTCGGCGTGTTCCGGGTGCTGGCGAAGAAAACGTTGTGCCTGGTCCAACGACGTAAAACGGGTAATCGCGCCCAGGACGACAGCTTCTTCATCACCATTACGTTGTTGCCAGTAGAAT > NC_000913/2380217‑2380488
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
