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 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,824,326 |
T→C |
100% |
pseudogene (459/687 nt) |
rph → |
ECK3633:JW3618:b3643; ribonuclease PH |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,824,326 | 0 | T | C | 100.0%
| 170.9
/ NA
| 51 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (24/27); total (24/27) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG > W3110S.gb/3824258‑3824392
|
aCGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc > 1:2596233/1‑71 (MQ=255)
aCGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc > 1:161265/1‑71 (MQ=255)
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:1440811/70‑1 (MQ=255)
cGGGTGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:251908/70‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:1129663/71‑1 (MQ=255)
tGCCTGCGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:2674295/71‑1 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg < 1:1695986/69‑1 (MQ=255)
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:752306/1‑71 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg < 1:2901685/67‑1 (MQ=255)
tGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATg < 1:346805/71‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:3179022/71‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:472549/71‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg < 1:3726898/65‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:60887/3‑70 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:1480384/50‑1 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg < 1:865652/54‑1 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt > 1:1362306/1‑71 (MQ=255)
cgcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:3728355/2‑56 (MQ=255)
cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCt > 1:1540956/1‑71 (MQ=255)
cTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa > 1:1816515/1‑46 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa < 1:3165651/45‑1 (MQ=255)
aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg > 1:3459713/1‑71 (MQ=255)
cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1798027/71‑1 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1738577/70‑1 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:2705041/70‑1 (MQ=255)
aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa > 1:1250514/1‑46 (MQ=255)
gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt < 1:3380871/48‑1 (MQ=255)
tggAAAACGGCGAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1348748/61‑1 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:1761834/59‑1 (MQ=255)
aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg < 1:973809/71‑3 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg > 1:3069060/1‑46 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAg > 1:1085990/1‑46 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTTTCGGTAtt < 1:530294/60‑1 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:687221/1‑68 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:2223891/1‑67 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:2065231/1‑67 (MQ=255)
cGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAg > 1:1117007/1‑71 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc < 1:1114151/71‑1 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:459703/71‑2 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg < 1:253506/51‑1 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa < 1:2483399/71‑3 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaa < 1:1545927/71‑3 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat < 1:618545/71‑4 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta > 1:3121599/1‑49 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta > 1:3560376/1‑49 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg < 1:394980/63‑3 (MQ=255)
gCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc > 1:81065/1‑36 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa > 1:3342808/1‑63 (MQ=255)
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:3640684/1‑71 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:1784038/1‑70 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCg < 1:2658297/70‑1 (MQ=255)
aaaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGa > 1:249979/1‑71 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:650640/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:3282768/1‑67 (MQ=255)
aaccaaccAGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGa > 1:2950482/1‑57 (MQ=255)
aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCt > 1:583756/1‑71 (MQ=255)
cAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg > 1:1385818/1‑70 (MQ=255)
|
ACGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG > W3110S.gb/3824258‑3824392
|
| 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
