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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,315,568 |
A→G |
51.9% |
G172G (GGT→GGC) |
ompC ← |
outer membrane porin protein C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,315,568 | 0 | A | G | 51.9%
| 5.8
/ 76.2
| 54 | G172G (GGT→GGC) | ompC | outer membrane porin protein C |
| Reads supporting (aligned to +/- strand): ref base A (16/10); new base G (13/15); total (29/25) |
| Fisher's exact test for biased strand distribution p-value = 2.90e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGT > W3110S.gb/2315506‑2315633
|
gCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTgg > 1:725759/1‑69 (MQ=255)
gCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTg > 1:3647165/1‑68 (MQ=255)
cGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGt > 1:1781238/1‑69 (MQ=255)
gACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGa < 1:2553123/68‑1 (MQ=255)
tgttAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCaa > 1:2681700/1‑69 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTAccc > 1:111336/1‑52 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTAccc > 1:2827013/1‑52 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTAccc > 1:1603227/1‑52 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTAccc > 1:2098474/1‑52 (MQ=255)
gttagttaCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTAcc > 1:223719/1‑51 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTa > 1:1339635/1‑42 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTa > 1:1476520/1‑42 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTa > 1:1864297/1‑42 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAgg > 1:352524/1‑69 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAgg > 1:2952326/1‑69 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAgg > 1:2017196/1‑69 (MQ=255)
aCGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAg > 1:1265703/1‑68 (MQ=255)
tAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:3404276/58‑1 (MQ=255)
tAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:17433/58‑1 (MQ=255)
tAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:2041530/58‑1 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:944820/57‑1 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:3518990/57‑1 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCa > 1:635000/1‑67 (MQ=255)
aGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGa < 1:3157406/46‑1 (MQ=255)
gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAg < 1:2522206/54‑1 (MQ=255)
gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAg < 1:3012761/54‑1 (MQ=255)
gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCa > 1:2610553/1‑66 (MQ=255)
gTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCa > 1:3639955/1‑66 (MQ=255)
gTAAAGCCTTCACCAGATGGCTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAg < 1:1290888/54‑1 (MQ=38)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:1664601/69‑1 (MQ=255)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:3173259/69‑1 (MQ=255)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCa < 1:2321199/68‑1 (MQ=255)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCa < 1:3313079/68‑1 (MQ=255)
aaaGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:2286998/69‑1 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGa > 1:1303269/1‑69 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGa > 1:220483/1‑69 (MQ=255)
aaGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:2242265/68‑1 (MQ=255)
aGCCTTCACCAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGtt < 1:2568933/52‑1 (MQ=255)
ccAGATGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCgaaga < 1:1904114/67‑1 (MQ=255)
cAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGaagaag < 1:1173264/68‑1 (MQ=255)
aGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:3175877/69‑1 (MQ=255)
gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCATACCGAAGAAGTCa > 1:1001767/1‑69 (MQ=255)
gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCa > 1:3166665/1‑69 (MQ=255)
gATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGACGTCAACCAGACCGAAGAAGtaa > 1:1891791/1‑67 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt > 1:281930/1‑69 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAgt > 1:3635668/1‑69 (MQ=255)
tGGGTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACAGAAGAAGTCAgt > 1:1302940/1‑69 (MQ=255)
gggTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCTAAGAAGTc < 1:2647829/65‑1 (MQ=255)
gggTTGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTc < 1:1083620/65‑1 (MQ=255)
tGCCGTTTTTGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTAc < 1:1873142/69‑1 (MQ=255)
cGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAg < 1:640165/46‑1 (MQ=255)
cGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg < 1:3024853/68‑1 (MQ=255)
tttGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg > 1:3530447/1‑64 (MQ=255)
tttGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg > 1:2428799/1‑64 (MQ=255)
tttGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg > 1:2223723/1‑64 (MQ=255)
tttGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACgg > 1:1811559/1‑64 (MQ=255)
tttGCCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGt > 1:848241/1‑69 (MQ=255)
|
GCGTCACGACCGTTGTTAGTTACGCCACTAGTAAAGCCTTCACCAGATGGGTTGCCGTTTTTACCCTGGTACTGAACAGCAAAGTTCAGGCCGTCAACCAGACCGAAGAAGTCAGTGTTACGGTAGGT > W3110S.gb/2315506‑2315633
|
| 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
