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 I1 R1
|
17 |
37.0 |
2377229 |
96.2% |
2286894 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
4,201,841 |
Δ1 bp |
coding (719/825 nt) |
iclR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 4,201,839 | 0 | A | . | 96.2%
| 116.1
/ ‑1.3
| 26 | coding (721/825 nt) | iclR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base . (10/15); total (10/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.42e-01 |
TCCTTCGCCGCTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGGAAATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCAACGTAGCCCCA > REL606/4201766‑4201907
|
tccttcGCCGCTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGGaat < 1:927748/76‑2 (MQ=255)
cttcGCCGCTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGGaatag < 2:1147647/76‑4 (MQ=255)
cgcTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTg < 2:379523/76‑1 (MQ=255)
cgcTTGAATCACCATAGCGCCAAGCTCGGTCACGCTGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTg < 2:379506/76‑1 (MQ=255)
cTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCg > 2:594673/1‑76 (MQ=255)
tAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCa < 1:234753/76‑1 (MQ=255)
aaTCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCaa < 1:726468/76‑1 (MQ=255)
aTCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCaaa < 2:622263/76‑1 (MQ=255)
cACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACg < 1:471058/76‑1 (MQ=255)
cgcCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACgg < 1:81369/76‑1 (MQ=255)
cgcCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACgg > 1:681844/1‑76 (MQ=255)
aaCTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTc < 1:31797/76‑1 (MQ=255)
tCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGGAAATAGAAATTGCGGCAAACGGTTCACGGTGCTCAt < 1:353197/76‑1 (MQ=255)
cGGTCACGCGGTCATCGGNAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCg < 1:939810/76‑1 (MQ=255)
ggTCACGCGGTCATCGGTAACACGTTAAATCGGT‑CGGGAATAGCAAGTGCGGCATACGGTTCACGGTGCTCATcta > 1:127474/1‑74 (MQ=255)
cACGCGGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGaaaa < 2:389861/76‑1 (MQ=255)
gcgGTCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATac > 2:111935/1‑76 (MQ=255)
gcgGTCATCGGTAATACCTGCAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATac < 2:165970/76‑1 (MQ=255)
tCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAATGGTTCACGCTGCTCATCGAAAATACACGc > 1:1077142/1‑76 (MQ=255)
tCATCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGc > 1:803032/1‑76 (MQ=255)
tCGGTAATACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCTCGGTGCTCATCGAAAATACACGCTGc < 1:111935/76‑1 (MQ=255)
gTAATACGTGAAATCGGTCCAG‑AATCGAAATTGCGACAAACGGTTCCCGGTGCTCATCGAAAATACACACTGCAAg > 1:132947/1‑76 (MQ=255)
aTACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGATAATACACGCTGCAAGGCa < 2:1080724/76‑1 (MQ=255)
aTACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGTAAGGCa < 1:1116572/76‑1 (MQ=255)
tACGTGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCaa > 2:525601/1‑76 (MQ=255)
tGAAATCGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCAACGTa > 2:711082/1‑76 (MQ=255)
aaaTCGGTCCGG‑AATAGAAAATGCGTCAAACGGTTAACGGTGCCCATCGAAAATACACGCTGCAAGGCTACGTacc > 1:127202/1‑74 (MQ=255)
cGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCAACGTAGCCCCa > 1:735055/1‑76 (MQ=255)
cGGTCCGG‑AATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCAACGTAGCCCCa < 1:293795/76‑1 (MQ=255)
|
TCCTTCGCCGCTTTAATCACCATTGCGCCAAACTCGGTCACGCGGTCATCGGTAATACGTGAAATCGGTCCGGAAATAGAAATTGCGGCAAACGGTTCACGGTGCTCATCGAAAATACACGCTGCAAGGCAACGTAGCCCCA > REL606/4201766‑4201907
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
