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 |
|
A5 F28 I2 R2
|
154 |
32.4 |
3140800 |
76.4% |
2399571 |
54.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,215,822 |
T→C |
intergenic (‑186/+19) |
ycgE ← / ← ycgF |
predicted DNA‑binding transcriptional regulator/predicted FAD‑binding phosphodiesterase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,215,822 | 0 | T | C | 76.5%
| 59.1
/ 14.4
| 34 | intergenic (‑186/+19) | ycgE/ycgF | predicted DNA‑binding transcriptional regulator/predicted FAD‑binding phosphodiesterase |
| Reads supporting (aligned to +/- strand): ref base T (5/3); new base C (0/26); total (5/29) |
| Fisher's exact test for biased strand distribution p-value = 2.01e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAC > W3110S.gb/1215762‑1215859
|
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:780785/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:385745/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:2963109/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:2898298/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:2041243/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:451784/1‑61 (MQ=255)
tAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCAtgt > 1:2130924/1‑61 (MQ=255)
tAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCATGTGAAAGAATGTGCTGaaa < 1:37134/62‑1 (MQ=255)
tAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCATGTGAAAGAATGTGCTGaaa < 1:780059/62‑1 (MQ=255)
tAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCATGTGAAAGAATGTGCCGaaa < 1:2575783/62‑1 (MQ=255)
cATTTTCACGATTATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:20144/50‑1 (MQ=25)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1993289/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1886279/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:469956/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:2385159/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:2598281/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:2605335/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:413373/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:2824163/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:2854490/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:3102456/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1863080/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1111888/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1855325/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1725969/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1147269/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:160339/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:5018/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:117265/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1288514/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1442807/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1434062/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1334619/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1418296/50‑1 (MQ=37)
cATTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1398603/50‑1 (MQ=37)
aTTTTCACGATGATTTCCAGAAATCATGCGAAATAATGTGCTGAAAatt < 1:1374992/49‑1 (MQ=37)
cATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAc > 1:315045/1‑42 (MQ=255)
cATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAc > 1:1422034/1‑42 (MQ=255)
cATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAc > 1:568415/1‑42 (MQ=255)
cATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAc > 1:2261512/1‑42 (MQ=255)
cATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAc > 1:1661049/1‑42 (MQ=255)
tgtgAAAGAATGTGCTGAAAATTATTTTTTCTCTg < 1:1930529/35‑1 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTggg > 1:58493/1‑35 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:2097822/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:3125884/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:29798/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:2809868/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:2806181/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1023980/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1540888/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1512434/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1366494/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1295910/1‑36 (MQ=255)
gtgAAAGAATGTGCTGAAAATTATTTTTTCTCTGGc > 1:1043190/1‑36 (MQ=255)
|
TAATGTGGATTAAATTTAAACGTAACGTATTCATTTTCACGATGATTTACTGAAATCATGTGAAAGAATGTGCTGAAAATTATTTTTTCTCTGGCCAC > W3110S.gb/1215762‑1215859
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
