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 |
|
A5 F21 I0 R1
|
148 |
22.8 |
1772010 |
97.0% |
1718849 |
61.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,410 |
T→A |
100% |
pseudogene (543/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,410 | 0 | T | A | 100.0%
| 66.5
/ NA
| 23 | pseudogene (543/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (11/12); total (11/12) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGA > W3110S.gb/3824343‑3824463
|
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGcc < 1:1393379/71‑1 (MQ=255)
gCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg < 1:1703197/70‑1 (MQ=255)
ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:1045583/71‑1 (MQ=255)
tttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCagag < 1:1086236/68‑1 (MQ=255)
cTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa < 1:1579603/70‑1 (MQ=255)
taaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:665352/3‑65 (MQ=255)
aaaCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtga > 1:662076/2‑71 (MQ=255)
aCGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGtgat > 1:1574406/1‑70 (MQ=255)
ggtgAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGAc > 1:1623345/4‑71 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:990184/35‑1 (MQ=255)
tttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1596225/51‑1 (MQ=255)
ttGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGgc > 1:836956/1‑71 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGCCCgcc > 1:1148913/1‑40 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAAc > 1:1638556/1‑48 (MQ=255)
tGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGa > 1:362667/1‑62 (MQ=255)
aTCTGTAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:1370258/59‑1 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:1543926/42‑1 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACg < 1:294634/42‑1 (MQ=255)
tGGAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCAtt > 1:1313625/1‑71 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGGTGACCGAAGACGGGCGCATCATTGa < 1:1435977/71‑1 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:1405789/1‑70 (MQ=255)
gAATACGTTGAAGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTg > 1:739328/1‑70 (MQ=255)
aaGACTCAGCCGCAGAGACCGACATGAACGTAGTGATGACCGaa < 1:898641/44‑1 (MQ=255)
|
TAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACATGAACGTAGTGATGACCGAAGACGGGCGCATCATTGA > W3110S.gb/3824343‑3824463
|
| 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
