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 |
3,824,326 |
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 | 98.0%
| 162.1
/ ‑4.4
| 50 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (25/24); total (26/24) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-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. |
CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG > W3110S.gb/3824259‑3824392
|
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)
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)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa > 1:355090/3‑55 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGcc < 1:127987/67‑1 (MQ=255)
gcaGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGc < 1:3551070/69‑1 (MQ=255)
caGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCg > 1:990850/2‑69 (MQ=255)
aGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATg < 1:419218/52‑1 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGc > 1:2839182/1‑63 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt < 1:1521966/71‑1 (MQ=255)
gcgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTc > 1:3011199/1‑71 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa < 1:429764/48‑1 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg < 1:1890847/71‑1 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg < 1:1406948/71‑1 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaa < 1:1613496/46‑1 (MQ=255)
tACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg < 1:3446359/69‑1 (MQ=255)
aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc > 1:1392742/1‑39 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAAccc < 1:3688770/37‑1 (MQ=255)
gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta < 1:1033110/71‑3 (MQ=255)
gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta > 1:237064/1‑69 (MQ=255)
aaGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg < 1:2049602/49‑1 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGAt > 1:2766624/1‑37 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt > 1:3415650/1‑71 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt > 1:2148388/1‑71 (MQ=255)
gCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAgg > 1:3054159/1‑42 (MQ=255)
ggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgta > 1:774020/1‑69 (MQ=255)
gtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtgtaa < 1:3620813/70‑3 (MQ=255)
tggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAAc < 1:3377709/71‑1 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAACGGGATGGTAGCCGCAGTTTCt < 1:2229462/54‑1 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTg > 1:1200252/1‑55 (MQ=255)
gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTCTAAACg < 1:474490/70‑1 (MQ=255)
aaaCGGCAAGCTGAAAACTAATCCAATGAAAGGGATGGTAGCCGCGGTCTCTGTCggga > 1:1077589/1‑57 (MQ=255)
aaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggta > 1:2831007/1‑56 (MQ=255)
aCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:3492240/1‑67 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat < 1:1612877/71‑4 (MQ=255)
aGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACgg > 1:1611622/1‑61 (MQ=255)
cTGAAAACCATCCCGATGAAAGGGATGGTAGCCGCAGtt < 1:3419264/39‑1 (MQ=37)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt < 1:3518798/39‑1 (MQ=255)
tGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATtg < 1:3631143/51‑1 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGc > 1:35930/1‑70 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGAt > 1:2383292/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTaaa > 1:1870317/1‑51 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc < 1:1369396/71‑1 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc > 1:561224/1‑71 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGCAAACGGTGAAGCAATTTGCGATc < 1:3040459/71‑1 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc > 1:1145129/1‑58 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc > 1:2886787/1‑58 (MQ=255)
ccAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATCTg > 1:982169/1‑71 (MQ=255)
|
CGGGTGCCTGCGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATCTG > W3110S.gb/3824259‑3824392
|
| 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
