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 |
|
A2 F8 I0 R1
|
82 |
77.9 |
2158605 |
86.8% |
1873669 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,658,643:1 |
+T |
100% |
coding (843/1542 nt) |
ppx → |
exopolyphosphatase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,658,643 | 1 | . | T | 97.8%
| 165.9
/ ‑2.9
| 46 | coding (843/1542 nt) | ppx | exopolyphosphatase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); new base T (45/0); total (46/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| 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. |
TTCCGGGACTGGCGATTTTATGCGGTGTG‑TTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACGG > minE/1658615‑1658684
|
ttCCGGGACTGGCGATTTTATGCGGTGTG‑TTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGa > 1:2098829/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:471868/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1008938/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:2018552/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:2126549/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:226665/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:23583/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:256124/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:299317/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:39367/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:398643/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:435578/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:2013754/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:528170/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:564189/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:60701/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:640895/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:654780/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:713607/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:751467/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:761364/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:846756/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:865721/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1369740/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1023368/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1072436/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1075287/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1093594/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1119104/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1153680/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:12313/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1250212/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:132234/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1365988/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:2000554/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1379826/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:140594/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1596817/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1744513/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:175252/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1844574/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1847037/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1892225/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1893819/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgg > 1:1895071/1‑67 (MQ=255)
gggACTGGCGATTTTATGCGGTGTGTTTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACgc > 1:625227/1‑66 (MQ=255)
|
TTCCGGGACTGGCGATTTTATGCGGTGTG‑TTTGATGCTTTAGCCATCCGTGAACTGCGCCTTTCTGACGG > minE/1658615‑1658684
|
| 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
