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 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,362 |
A→T |
100% |
pseudogene (495/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,362 | 0 | A | T | 100.0%
| 121.6
/ NA
| 43 | pseudogene (495/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (27/16); total (27/16) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACAT > W3110S.gb/3824294‑3824427
|
aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt < 1:1753082/71‑1 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg > 1:794802/1‑71 (MQ=255)
cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa > 1:838214/1‑63 (MQ=255)
cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg > 1:1538054/1‑71 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTg > 1:2184014/1‑71 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCATTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa < 1:1100532/71‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:188839/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa < 1:196637/71‑1 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa < 1:1160993/70‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg > 1:2304483/1‑71 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1455672/71‑1 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:2576568/71‑1 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:1520686/71‑1 (MQ=255)
aacccGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg > 1:696521/4‑70 (MQ=255)
cGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:470172/60‑1 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt > 1:81868/1‑70 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt > 1:2717838/1‑70 (MQ=255)
gAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGtt > 1:213824/1‑70 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa < 1:2386144/49‑3 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:1714086/70‑1 (MQ=255)
aaaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg > 1:2375018/1‑70 (MQ=255)
aaGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:507086/1‑62 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:1430861/1‑67 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGa > 1:494218/1‑66 (MQ=255)
gATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGAct > 1:1585396/1‑71 (MQ=255)
aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa < 1:1600943/66‑1 (MQ=255)
aTGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGaa > 1:1795584/1‑66 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGActcag > 1:671196/1‑68 (MQ=255)
gTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGc > 1:1538357/1‑71 (MQ=255)
tAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTg < 1:1956780/60‑1 (MQ=255)
ccGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCa < 1:2158226/71‑1 (MQ=255)
gTTTCTGTCGTTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:2031462/43‑1 (MQ=16)
gTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTgg < 1:2558522/43‑1 (MQ=19)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:2492081/1‑43 (MQ=19)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc > 1:1584950/1‑69 (MQ=255)
ttCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGAc > 1:1915809/1‑69 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1762086/1‑42 (MQ=19)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1961018/1‑42 (MQ=19)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGaa > 1:1962230/1‑42 (MQ=19)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCg > 1:2061158/1‑61 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:356029/1‑71 (MQ=255)
tCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGa > 1:2554497/1‑71 (MQ=255)
tCGGTATTGTAAACGGTGAAGCAATTTGCGATCTGGAATACGTTGAAGACTCAGCCGCAGAGACCGACAt > 1:324375/1‑70 (MQ=255)
|
AAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTGGAATACGTTGAAGACTCTGCCGCAGAGACCGACAT > W3110S.gb/3824294‑3824427
|
| 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
