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 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,111,828:1 |
+C |
100% |
coding (917/1536 nt) |
mdoG → |
glucan biosynthesis protein, periplasmic |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,111,828 | 1 | . | C | 75.0%
| 14.9
/ 1.6
| 8 | coding (917/1536 nt) | mdoG | glucan biosynthesis protein, periplasmic |
| Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (6/0); total (6/2) |
| Fisher's exact test for biased strand distribution p-value = 3.57e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.17e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| 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. |
AATGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAA‑CCCGCAAGGCTTTGGTCTGTTGCAGCGCGGTCGTGATTTCTCCCGCTTTGAAGATCTCGATG > W3110S.gb/1111758‑1111890
|
aaTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa > 1:1156066/1‑71 (MQ=255)
aaTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa > 1:677358/1‑71 (MQ=255)
aaTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa > 1:660971/1‑71 (MQ=255)
aaTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa > 1:1614999/1‑71 (MQ=255)
aTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa < 1:118011/70‑1 (MQ=255)
aTGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGaaaa < 1:1587185/70‑1 (MQ=255)
ggCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAA‑ccc > 1:1512320/1‑71 (MQ=255)
ggCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAA‑ccc > 1:393033/1‑71 (MQ=255)
ggCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAA‑cc > 1:974721/1‑70 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgcg > 1:1478/1‑71 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgcg > 1:1454809/1‑71 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgcg > 1:1379599/1‑71 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgcg > 1:1251727/1‑71 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgcg > 1:734700/1‑71 (MQ=255)
aTAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAACCCCGCAAGGCTTTGGTCTGTTGCAgc > 1:748839/1‑70 (MQ=255)
cATGGAAAA‑CCCGCAAGGCTTTGGTCTGTTGCAGCGCGGTCGTGATTTCTCCCGCTTTGAAGATCTCgatg < 1:438061/71‑1 (MQ=255)
cATGGAAAA‑CCCGCAAGGCTTTGGTCTGTTGCAGCGCGGTCGTGATTTCTCCCGCTTTGAAGATCTCgatg < 1:1246765/71‑1 (MQ=255)
|
AATGGCGAATGGATCTGGCGTCCGTTGAATAACCCGAAACATTTAGCGGTCAGCAGCTTCTCCATGGAAAA‑CCCGCAAGGCTTTGGTCTGTTGCAGCGCGGTCGTGATTTCTCCCGCTTTGAAGATCTCGATG > W3110S.gb/1111758‑1111890
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
