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 |
|
A79 F1 I1 R1
|
19 |
52.0 |
3333102 |
95.7% |
3189778 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,222,511 |
C→T |
R200C (CGT→TGT) |
rtn → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,222,511 | 0 | C | T | 97.1%
| 124.7
/ ‑3.1
| 34 | R200C (CGT→TGT) | rtn | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (23/10); total (23/11) |
| Fisher's exact test for biased strand distribution p-value = 3.24e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.25e-01 |
CGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCCTCTG > REL606/2222445‑2222579
|
cGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTtgatga > 2:127079/1‑76 (MQ=255)
cGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTtgatga < 2:301888/76‑1 (MQ=255)
aGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGt > 1:681683/1‑76 (MQ=255)
aaGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTaa > 2:114412/1‑76 (MQ=255)
aaGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTaa > 2:607128/1‑76 (MQ=255)
gATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACg < 2:945142/76‑1 (MQ=255)
ttACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGaa > 2:774641/1‑76 (MQ=255)
ttACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGaa > 2:774648/1‑76 (MQ=255)
gCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGa < 1:487078/76‑1 (MQ=255)
cGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATg < 2:422621/76‑1 (MQ=255)
cGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATg > 2:908447/1‑76 (MQ=255)
cTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAg > 1:985742/1‑76 (MQ=255)
tattGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGt < 1:1614122/76‑1 (MQ=255)
attGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTg < 2:1298463/76‑1 (MQ=255)
attGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTg > 1:501985/1‑76 (MQ=255)
tGGCAATACTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGaa > 1:587831/1‑76 (MQ=255)
gcTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTaaaa > 1:1127007/2‑76 (MQ=255)
cTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAAt > 1:845728/1‑76 (MQ=255)
cTGCGCTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAAt > 1:1345832/1‑76 (MQ=255)
gcgcTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTg < 2:1490687/76‑1 (MQ=255)
gcTATCTGCCTTTTCTTCATGTTTGATGAACGTTAACGAATAACCCGACATGCCAGTCCGTGAAACTAAAATTGCg < 2:713339/76‑1 (MQ=255)
cTATCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCgg > 1:1282540/1‑76 (MQ=255)
tATCTGCCTTTTCTTCATGTTTGAGGAACGTTAACGAATTAACCGACAGGCCAGTCCGTGAAACTAAAATTGCggg < 1:613263/76‑1 (MQ=255)
aTCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGc > 1:241367/1‑76 (MQ=255)
aTCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGc > 1:221219/1‑76 (MQ=255)
aTCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGc > 2:1318642/1‑76 (MQ=255)
aTCTACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGc < 1:1418178/76‑1 (MQ=255)
tACCTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCAtt > 2:338127/1‑76 (MQ=255)
ccTTTTCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGACCGCGAAACTAAAATTGCGGGCATTcc > 2:864728/1‑76 (MQ=255)
ttttCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCctc < 2:919136/76‑1 (MQ=255)
tttCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCctct > 1:653009/1‑76 (MQ=255)
tttCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCctct < 1:1391064/76‑1 (MQ=255)
tttCTTCATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCctct < 1:1007759/76‑1 (MQ=255)
ttcttcATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCCTCTg > 1:1554683/1‑76 (MQ=255)
ttcttcATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCCTCTg > 1:1587982/1‑76 (MQ=255)
ttcttcATGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCCTCTg > 1:179160/1‑76 (MQ=255)
|
CGGCAGGAAGATTACGATGGCGTCGCCCTCATTATTGGCAATACTGCGCTATCTACCTTTTCTTCACGTTTGATGAACGTTAACGAATTAACCGACATGCCAGTCCGTGAAACTAAAATTGCGGGCATTCCTCTG > REL606/2222445‑2222579
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
