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 F21 I0 R1
|
148 |
22.8 |
1772010 |
97.0% |
1718849 |
61.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
711,161 |
C→T |
100% |
intergenic (‑93/+196) |
fur ← / ← fldA |
DNA‑binding transcriptional dual regulator/flavodoxin 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 711,161 | 0 | C | T | 76.5%
| 26.6
/ 6.4
| 17 | intergenic (‑93/+196) | fur/fldA | DNA‑binding transcriptional dual regulator/flavodoxin 1 |
| Reads supporting (aligned to +/- strand): ref base C (3/1); new base T (5/8); total (8/9) |
| Fisher's exact test for biased strand distribution p-value = 2.94e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTA > W3110S.gb/711097‑711221
|
cACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTa > 1:497282/1‑70 (MQ=255)
aCTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTaaa < 1:395925/71‑1 (MQ=255)
tCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCAc < 1:28108/61‑1 (MQ=255)
cATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGa > 1:685580/1‑70 (MQ=255)
tGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTcc < 1:14513/71‑1 (MQ=255)
gACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTccc > 1:1240730/1‑71 (MQ=255)
aGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAAt < 1:291427/52‑1 (MQ=255)
gAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAAt < 1:406842/51‑1 (MQ=255)
aaTTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCa < 1:1419539/71‑1 (MQ=255)
aTGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCaaa > 1:1722728/1‑56 (MQ=255)
cGTATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACg < 1:974982/70‑1 (MQ=255)
tATCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACg < 1:1051162/68‑1 (MQ=255)
tCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGt > 1:1711165/1‑55 (MQ=255)
tCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca > 1:240571/1‑71 (MQ=255)
tCATTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca > 1:1337264/1‑71 (MQ=255)
aTTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGcaca < 1:1026963/71‑1 (MQ=255)
aTTATAGAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGca > 1:1355453/1‑69 (MQ=255)
gAATTGCCATGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTa < 1:607600/70‑1 (MQ=255)
|
CACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCCACGCCTAAATGAAAACCACAAGTCCCTGGCAAATATTGTTAATAAAAACGTGGCACAGCTTA > W3110S.gb/711097‑711221
|
| 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
