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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,417,935 |
G→A |
35.2% |
H241H (CAC→CAT) |
rffM ← |
UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,417,935 | 0 | G | A | 35.2%
| 33.2
/ 26.4
| 51 | H241H (CAC→CAT) | rffM | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| Reads supporting (aligned to +/- strand): ref base G (30/3); new base A (12/6); total (42/9) |
| Fisher's exact test for biased strand distribution p-value = 5.20e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01 |
CAGACAGGCGACGGAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAGG > minE/2417868‑2417998
|
cAGACAGGCGACGGAGTGACCTCTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGt > 1:3156516/1‑69 (MQ=255)
cAGACAGGCGACGGAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAg > 1:3212101/1‑68 (MQ=255)
cAGACAGGCGACGGAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGt > 1:3135647/1‑69 (MQ=255)
ggAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAAt > 1:2549279/1‑69 (MQ=255)
ggAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAAt > 1:2069203/1‑69 (MQ=255)
ggAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAAt > 1:52787/1‑69 (MQ=255)
ggAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAAt > 1:2747097/1‑69 (MQ=255)
ggAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAAt > 1:1965933/1‑69 (MQ=255)
aCCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgc > 1:59971/1‑68 (MQ=255)
aCCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgc > 1:1618617/1‑68 (MQ=255)
ccACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgca > 1:753011/1‑68 (MQ=255)
ccACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgca > 1:515936/1‑68 (MQ=255)
ccACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgca > 1:1677762/1‑68 (MQ=255)
ccACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgca > 1:1998000/1‑68 (MQ=255)
cACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACgcag > 1:2218177/1‑68 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGt > 1:1207917/1‑45 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTa > 1:2916927/1‑54 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTa > 1:3389017/1‑54 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTa > 1:933892/1‑54 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTa > 1:2660724/1‑54 (MQ=255)
ccGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTa > 1:1521956/1‑54 (MQ=255)
cGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAg < 1:2298369/69‑1 (MQ=255)
cGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAg < 1:2010830/69‑1 (MQ=255)
gCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAg < 1:589842/68‑1 (MQ=255)
cAAAGAGAGGAAAATCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:974385/67‑1 (MQ=255)
cAAAGAGAGGAAAATCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:943031/67‑1 (MQ=255)
cAAAGAGAGGAAAATCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:1806321/67‑1 (MQ=255)
cAAAGAGAGGAAAATCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:2754115/67‑1 (MQ=255)
cAAAGAGAGGAAAATCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:2019878/67‑1 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:26694/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:2251683/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:894094/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:793544/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:1347614/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:70037/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:1592821/1‑69 (MQ=255)
aaaaTCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggc > 1:1943476/1‑69 (MQ=255)
aaaTCAGAGGTTGCCGGTGTAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGAc < 1:501812/56‑1 (MQ=255)
cATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggctcggc > 1:2176625/1‑69 (MQ=255)
cATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGcggctcggc > 1:3125353/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAAGGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:707335/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:426663/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:3301014/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:2549192/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:2521741/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:1381560/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:1932278/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:1198591/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:821455/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:1223670/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:2429694/1‑69 (MQ=255)
gtgtAATGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAgg > 1:2017966/1‑69 (MQ=255)
|
CAGACAGGCGACGGAGTGACCACTCCGTCGCTTTACAAAGAGAGGAAAATCATAGGTTGCCGGTGTAGTGCCAGCGTAAATAACGCAGCAAACGAAGCTGACGCTTAATGCGGCTCGGCTGCGAAAGCAGG > minE/2417868‑2417998
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
