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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,428,262:1 |
+G |
100% |
coding (735/855 nt) |
ulaE → |
L‑xylulose 5‑phosphate 3‑epimerase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,428,262 | 1 | . | G | 75.0%
| 72.0
/ 16.9
| 28 | coding (735/855 nt) | ulaE | L‑xylulose 5‑phosphate 3‑epimerase |
| Reads supporting (aligned to +/- strand): ref base . (0/7); new base G (8/13); total (8/20) |
| Fisher's exact test for biased strand distribution p-value = 7.49e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. |
ACGTGCCGTTTGGCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGACCCGGCGGCAGAAGTGGCGAA > W3110S.gb/4428192‑4428324
|
aCGTGCCGTTTGGCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGc > 1:1351798/1‑71 (MQ=255)
aCGTGCCGTTTGGCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGc > 1:1936025/1‑71 (MQ=255)
aCGTGCCGTTTGGCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGc > 1:3563108/1‑71 (MQ=255)
gCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCt < 1:1031894/71‑1 (MQ=255)
gCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCt < 1:1682040/71‑1 (MQ=255)
gCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCt < 1:3196052/71‑1 (MQ=255)
gCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCt < 1:310418/71‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTga < 1:634006/71‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTga < 1:531648/71‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTga < 1:3614086/70‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTga < 1:179923/70‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTga < 1:3444055/70‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTga < 1:307615/70‑1 (MQ=255)
gtgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTga < 1:2970089/70‑1 (MQ=255)
tgtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTga < 1:1442958/70‑1 (MQ=255)
gtAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGa > 1:1342419/1‑65 (MQ=255)
tAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTgaga < 1:3689957/70‑1 (MQ=255)
gTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGAtgt > 1:761169/1‑71 (MQ=255)
gATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGAtgtg > 1:3508565/1‑69 (MQ=255)
gATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGAtgtg > 1:1585388/1‑69 (MQ=255)
gATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGAtgtg > 1:817559/1‑69 (MQ=255)
ttCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGc > 1:876158/1‑70 (MQ=255)
gAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGaa < 1:2609815/70‑1 (MQ=255)
gAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGaa < 1:2066875/70‑1 (MQ=255)
gAACCTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGaa < 1:30278/70‑1 (MQ=255)
tttCGAAACGCTCAAACAGAGTGGCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGaa < 1:86432/71‑1 (MQ=255)
aaaCAGAGTGGCTATTGC‑GGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGACCCGGCGTCAGa < 1:1736798/71‑1 (MQ=255)
aaaCAGAGTGGCTATTGC‑GGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGACCCGGCGGCAGa < 1:2488416/71‑1 (MQ=255)
gCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGTAAGAcc > 1:2168856/1‑52 (MQ=37)
gCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGAcc > 1:1523099/1‑52 (MQ=38)
gCTATTGCGGGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGACCCGGCGGCAGAAGTGGCGaa < 1:2246567/71‑1 (MQ=255)
|
ACGTGCCGTTTGGCGAAGGTGTAGTGGATTTCGAACGTTGTTTCGAAACGCTCAAACAGAGTGGCTATTGC‑GGGCCGTACCTGATTGAGATGTGGAGCGAAACGGCGGAAGACCCGGCGGCAGAAGTGGCGAA > W3110S.gb/4428192‑4428324
|
| 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
