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 |
|
A1 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,291,041 |
A→G |
50.9% |
L791L (CTA→CTG) |
yraJ → |
predicted outer membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,291,041 | 0 | A | G | 50.9%
| ‑0.9
/ 76.2
| 53 | L791L (CTA→CTG) | yraJ | predicted outer membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (10/16); new base G (16/11); total (26/27) |
| Fisher's exact test for biased strand distribution p-value = 1.73e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01 |
CCCTTTGGCGCTCTTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAGGCAGATCAAC > W3110S.gb/3290973‑3291108
|
cccTTTGGCGCTCTTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACtata < 1:2263041/71‑1 (MQ=255)
ccTTTGGCGCTCTTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACtata < 1:2163985/70‑1 (MQ=255)
ggCGCTCTTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGGATACTGTAtctctc > 1:2743671/1‑71 (MQ=255)
ctTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGa > 1:312313/1‑70 (MQ=255)
gCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATc > 1:2085678/1‑71 (MQ=255)
cAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATc > 1:1930241/1‑69 (MQ=255)
cAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATc > 1:1887882/1‑69 (MQ=255)
cAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTa < 1:2721369/71‑1 (MQ=255)
cAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTa < 1:268181/71‑1 (MQ=255)
cGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTaa < 1:2103777/69‑1 (MQ=255)
cGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAAt < 1:889010/71‑1 (MQ=255)
gatgatACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAAt > 1:178399/1‑70 (MQ=255)
atgatACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATc > 1:652076/1‑70 (MQ=255)
cGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGc < 1:1843998/71‑1 (MQ=255)
gggCAACAAAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTg < 1:1173269/71‑1 (MQ=255)
caacaaAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAAt > 1:2718717/1‑58 (MQ=255)
caacaaAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAAt > 1:1151266/1‑58 (MQ=255)
caacaaAGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAAt > 1:2715469/1‑58 (MQ=255)
acaaAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAg > 1:1219630/1‑51 (MQ=255)
acaaAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATca < 1:540204/58‑1 (MQ=255)
acaaAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACaaa > 1:467221/1‑62 (MQ=255)
caaAGTATCGTCGATGAGGGCGGCATACTGTAtctctc > 1:513284/1‑38 (MQ=255)
caaAGTATCGTCGATGAGGGCGGCATACTGTAtctctc > 1:1211216/1‑38 (MQ=255)
caaAGTATCGTCGATGAGG‑‑GGCATACTGTAtctctc > 1:661609/1‑36 (MQ=21)
aaaGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTa > 1:1805784/1‑71 (MQ=255)
aaGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGa > 1:1101128/1‑41 (MQ=255)
aaGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTAc > 1:2196083/1‑71 (MQ=255)
aGTATCGTCGATGAGGGCGGCATACTGTATCTCTCTgg < 1:704311/38‑1 (MQ=255)
tcgtcgATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAAt < 1:2647064/48‑1 (MQ=255)
tcgtcgATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTg < 1:598554/70‑1 (MQ=255)
tcgtcgATGAGGGCGGCATACTATATCTCTCTGGGATATCg < 1:2748314/41‑1 (MQ=255)
gtcgATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTggg > 1:1058527/1‑70 (MQ=255)
gtcgATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTggg > 1:434927/1‑70 (MQ=255)
tcgATGAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATcac < 1:2741471/48‑1 (MQ=255)
tcgATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACaaa < 1:698578/51‑1 (MQ=255)
tcgATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGa < 1:1739386/71‑1 (MQ=255)
tcgATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGa < 1:240061/71‑1 (MQ=255)
aTGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAAt < 1:2250026/71‑1 (MQ=255)
tGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAAt < 1:20025/70‑1 (MQ=255)
tGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAAt < 1:1592008/70‑1 (MQ=255)
gAGGGCGGCATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAAt > 1:422184/1‑69 (MQ=255)
aGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAg < 1:2463414/71‑1 (MQ=255)
aGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAg > 1:2295139/1‑71 (MQ=255)
ggcggcATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCa > 1:127495/1‑68 (MQ=255)
ggcggcATACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAgg > 1:1261675/1‑70 (MQ=255)
cATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAGGCAGAta < 1:1178683/71‑2 (MQ=255)
tACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTg < 1:2684920/40‑1 (MQ=255)
tACTGTATCTCTCTGGGATATCGAGTAAATCACAAAGCTg < 1:199343/40‑1 (MQ=255)
tACTGTATCTCTCTGGGATATCGAGTAAATCACAAACCTg < 1:2323566/40‑1 (MQ=38)
tACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGt < 1:619314/46‑1 (MQ=255)
tACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGt < 1:1133973/46‑1 (MQ=255)
tACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCa < 1:2632388/61‑1 (MQ=255)
cTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGa > 1:2549912/1‑40 (MQ=255)
cTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAGGCAGATcaac < 1:2699778/70‑1 (MQ=255)
cTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAGGCAGATcaac > 1:1262326/1‑70 (MQ=255)
|
CCCTTTGGCGCTCTTGCCAGCAACGATGATACGGGGCAACAAAGTATCGTCGATGAGGGCGGCATACTATATCTCTCTGGGATATCGAGTAAATCACAAAGCTGGACTGTACGCTGGGGAAATCAGGCAGATCAAC > W3110S.gb/3290973‑3291108
|
| 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
