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 F1 I0 R1
|
44 |
27.8 |
2109400 |
97.8% |
2062993 |
62.3 |
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%
| 86.5
/ NA
| 25 | pseudogene (459/687 nt) | rph | ECK3633:JW3618:b3643; ribonuclease PH |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/15); total (10/15) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATC > W3110S.gb/3824269‑3824390
|
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGa < 1:489524/71‑1 (MQ=255)
gTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGAt < 1:6448/71‑1 (MQ=255)
gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATgg < 1:731059/70‑1 (MQ=255)
aTGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGtt < 1:396857/71‑1 (MQ=255)
tGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg < 1:2054738/62‑1 (MQ=255)
cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:527092/1‑50 (MQ=255)
gcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa > 1:59868/1‑49 (MQ=255)
aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:302186/46‑1 (MQ=255)
aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGaaa < 1:2105073/46‑1 (MQ=255)
aCAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCg > 1:1196691/1‑71 (MQ=255)
aGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCgg > 1:1666735/1‑70 (MQ=255)
aGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt > 1:1095429/1‑71 (MQ=255)
aaaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt < 1:855431/71‑2 (MQ=255)
aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg < 1:1762149/71‑3 (MQ=255)
aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt > 1:1592648/1‑69 (MQ=255)
aaaCGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggt > 1:866780/1‑69 (MQ=255)
ggCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGc < 1:700526/71‑1 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCggt < 1:1945125/53‑2 (MQ=255)
gCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca < 1:1241079/71‑2 (MQ=255)
cAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGca > 1:278509/1‑69 (MQ=255)
aaGCTGAAAACCAACCCGATTAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat < 1:2031320/71‑4 (MQ=255)
aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAt > 1:1361155/1‑53 (MQ=255)
cTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTAtt < 1:1372368/51‑1 (MQ=255)
gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGt < 1:72774/42‑1 (MQ=255)
aaaCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACggtg > 1:315460/1‑55 (MQ=255)
aaccaaccCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGCAATTTGCGATc < 1:777151/71‑1 (MQ=255)
|
CGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGTTTGCGATC > W3110S.gb/3824269‑3824390
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
