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 |
|
A3 F1 I1 R1
|
781 |
46.9 |
2231650 |
93.5% |
2086592 |
109.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,039,654 |
(C)5→4 |
coding (177/1005 nt) |
yedY → |
membrane‑anchored, periplasmic TMAO, DMSO reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,039,650 | 0 | C | . | 91.3%
| 77.5
/ 2.5
| 23 | coding (173/1005 nt) | yedY | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| Reads supporting (aligned to +/- strand): ref base C (1/1); new base . (10/11); total (11/12) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.67e-01 |
ACGGCCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCC > NC_000913/2039514‑2039776
|
aCGGCCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCgcccgcccgccc < 1:183170/139‑1 (MQ=255)
gTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGaa > 2:941238/1‑139 (MQ=255)
ggTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAg < 2:865428/139‑1 (MQ=255)
ttATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAg < 1:941238/139‑1 (MQ=255)
gCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTg > 2:236922/1‑139 (MQ=255)
ttAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCt > 2:469888/1‑139 (MQ=255)
aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa > 2:378536/1‑139 (MQ=255)
aCTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATa > 1:831475/1‑139 (MQ=255)
tGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAgcgc < 1:139887/104‑1 (MQ=255)
tGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAgcgc > 2:139887/1‑104 (MQ=255)
aCTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGcc < 2:420223/139‑1 (MQ=255)
cTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTcc < 1:236922/139‑1 (MQ=255)
tCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg < 1:821799/139‑1 (MQ=255)
cACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCg < 1:469888/139‑1 (MQ=255)
aCGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCgcccgcccgccc < 1:858455/57‑1 (MQ=255)
aCGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCgcccgcccgccc > 2:858455/1‑57 (MQ=255)
aCGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGt > 1:1112381/1‑139 (MQ=255)
cgcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataat < 1:378536/139‑1 (MQ=255)
gcATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTataata < 2:1106449/139‑1 (MQ=255)
gCTGGTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg < 1:820681/139‑1 (MQ=255)
gTTTAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTgg > 2:481034/1‑139 (MQ=255)
ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg > 2:1013773/1‑133 (MQ=255)
ttAAAGGGAACGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg < 1:1013773/133‑1 (MQ=255)
aaCGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGcc < 2:1092475/82‑1 (MQ=255)
aaCGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGcc > 1:1092475/1‑82 (MQ=255)
aaCGATCGCCCGCCCG‑CCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGa > 2:840101/1‑139 (MQ=255)
gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg > 2:40342/1‑118 (MQ=255)
gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCggg < 1:40342/118‑1 (MQ=255)
gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATcc < 2:379098/135‑1 (MQ=255)
gcccgcccg‑cccCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATcc > 1:379098/1‑135 (MQ=255)
|
ACGGCCGAGTCGGTATTCTTTATGAAGCGTCGGCAGGTGTTAAAAGCACTGGGCATCAGTGCAACTGCACTTTCTTTGCCTCACGCTGCGCATGCCGATCTGCTTAGCTGGTTTAAAGGGAACGATCGCCCGCCCGCCCCCGCCGGAAAAGCGCTGGAGTTCAGCAAGCCTGCCGCCTGGCAAAATAACCTGCCACTGACGCCAGCAGATAAAGTTTCCGGTTATAATAACTTCTATGAATTCGGGCTGGATAAAGCCGATCC > NC_000913/2039514‑2039776
|
| 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
