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 F1 I0 R1
|
92 |
46.1 |
3712835 |
96.9% |
3597737 |
60.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,280 |
T→C |
100% |
pseudogene (413/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,280 | 0 | T | C | 100.0%
| 149.4
/ NA
| 45 | pseudogene (413/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (19/26); total (19/26) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGG > W3110S.gb/3824216‑3824342
|
gACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:400451/71‑1 (MQ=255)
cGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgcgc > 1:507679/1‑71 (MQ=255)
tGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa < 1:2377534/71‑1 (MQ=255)
cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCTCTGGCAGATGCGCTACa < 1:166915/71‑1 (MQ=255)
cTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTa > 1:1998570/1‑69 (MQ=255)
gCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAg < 1:535315/55‑1 (MQ=255)
tGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtgg > 1:571786/1‑71 (MQ=255)
tGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtgg > 1:1284458/1‑71 (MQ=255)
ggtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCtggtgg > 1:61511/1‑70 (MQ=255)
gtggCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaa < 1:450708/71‑1 (MQ=255)
gCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAAc < 1:1459301/71‑1 (MQ=255)
aCGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACgg > 1:1365614/1‑71 (MQ=255)
cgcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATgc < 1:407187/46‑1 (MQ=255)
gcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGa < 1:1500725/53‑1 (MQ=255)
gcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCa < 1:1920139/71‑1 (MQ=255)
gcgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCa < 1:891964/71‑1 (MQ=255)
cgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGaaaa > 1:2355758/1‑65 (MQ=255)
cgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAAc > 1:3536112/1‑66 (MQ=255)
cgTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGc > 1:621850/1‑69 (MQ=255)
ccGCGTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCt < 1:3687798/70‑1 (MQ=255)
cgcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACg < 1:1781495/62‑1 (MQ=255)
gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaa < 1:434058/71‑1 (MQ=255)
gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaa < 1:950782/71‑1 (MQ=255)
gcgTCGATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaa < 1:2056591/71‑1 (MQ=255)
gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc < 1:2258639/70‑1 (MQ=255)
gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc > 1:3138298/1‑70 (MQ=255)
gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc < 1:195325/70‑1 (MQ=255)
gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc > 1:791620/1‑70 (MQ=255)
gATTACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCa < 1:861799/71‑1 (MQ=255)
gATTACGGGTGCCTGCGTCGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGaaa > 1:2975820/1‑67 (MQ=255)
tACGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCaacc > 1:2074236/1‑69 (MQ=255)
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:2075261/70‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:1090801/71‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:1028169/71‑1 (MQ=255)
tGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:3123781/1‑69 (MQ=255)
tcGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:1306615/2‑68 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAggg < 1:3157318/70‑1 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:1585929/1‑71 (MQ=255)
gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTg < 1:605349/48‑1 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt < 1:2872901/70‑1 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt < 1:997049/70‑1 (MQ=255)
ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg > 1:559749/1‑71 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg > 1:1672456/1‑70 (MQ=255)
cgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg > 1:2979330/1‑69 (MQ=255)
tGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAAcc < 1:2578401/47‑1 (MQ=255)
|
GACGTGCTTCAGGCTGATGGTGGCACGCGTACCGCGTCGATTACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGG > W3110S.gb/3824216‑3824342
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
