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 |
|
A57 F1 I1 R1
|
16 |
65.9 |
4148770 |
97.1% |
4028455 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,842,751 |
A→C |
L447W (TTG→TGG) |
dnaA ← |
chromosomal replication initiation protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,842,751 | 0 | A | C | 95.2%
| 256.6
/ 1.5
| 62 | L447W (TTG→TGG) | dnaA | chromosomal replication initiation protein |
| Reads supporting (aligned to +/- strand): ref base A (1/2); new base C (32/27); total (33/29) |
| Fisher's exact test for biased strand distribution p-value = 5.95e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.52e-01 |
CATAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCAACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCGCCAATCTCCG > REL606/3842680‑3842823
|
naTAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTg > 1:341076/2‑76 (MQ=255)
cATAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTg < 1:574549/76‑1 (MQ=255)
tAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCt < 2:1577103/76‑1 (MQ=255)
tAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCt > 1:354489/1‑76 (MQ=255)
tAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCt < 1:84878/76‑1 (MQ=255)
aGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTc < 1:1436153/76‑1 (MQ=255)
ggTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCAACTGCTCg < 2:1763339/76‑1 (MQ=255)
gTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGa > 2:1146867/1‑76 (MQ=255)
ttACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATc > 1:1535023/1‑76 (MQ=255)
aCGATGATAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCtt > 1:431498/1‑76 (MQ=255)
aCGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCtt < 2:647408/76‑1 (MQ=255)
cGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTa > 2:2042317/1‑76 (MQ=255)
gATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTAc < 1:477456/76‑1 (MQ=255)
aTGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACg < 2:103896/76‑1 (MQ=255)
aTGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACg < 1:207625/76‑1 (MQ=255)
tGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACgg < 1:127133/76‑1 (MQ=255)
tGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACgg < 1:466090/76‑1 (MQ=255)
gACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTTCTCGATCTTACggc < 2:92729/76‑1 (MQ=255)
gACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACggc > 1:1738523/1‑76 (MQ=255)
aCAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACggca < 2:354489/76‑1 (MQ=255)
aTGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACggcaggc > 2:912806/1‑76 (MQ=255)
tGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACggcaggca > 2:1298780/1‑76 (MQ=255)
tGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAg > 1:1023274/1‑76 (MQ=255)
tGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAg > 1:1746357/1‑76 (MQ=255)
gATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGc < 2:1480503/76‑1 (MQ=255)
aTTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCa > 2:613012/1‑76 (MQ=255)
aTTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCa > 1:470601/1‑76 (MQ=255)
tAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCCTACGGCAGGCATGAAGCAcc > 1:499590/1‑76 (MQ=255)
aaaTTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACcg > 1:1121682/1‑76 (MQ=255)
aTTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACcgtc < 2:1175661/76‑1 (MQ=255)
ttGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACcgtcgt > 1:1314070/1‑76 (MQ=255)
ttGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACcgtcgt > 2:1292205/1‑76 (MQ=255)
ttGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACcgtcgt > 1:82217/1‑76 (MQ=255)
gAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCgtgg > 1:608818/1‑75 (MQ=255)
aaaaaTCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGGCgtggg > 1:1129938/1‑74 (MQ=255)
aaTCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTc < 2:490468/76‑1 (MQ=255)
aTCTTCTTTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCa < 1:624430/76‑1 (MQ=255)
tcttctTTGATATCGTGGCTCTCTTCACGCAACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCAc < 1:1140754/76‑1 (MQ=255)
cttcttTGATATCCTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACg < 1:1248168/76‑1 (MQ=255)
cttTGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑cc > 2:760309/1‑76 (MQ=255)
tGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGGATGAAGCACCGTCGTGTGGTCACGG‑ccccc > 2:598187/1‑76 (MQ=255)
tGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑ccacc < 1:480469/76‑1 (MQ=255)
tGATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑ccacc > 2:1856775/1‑76 (MQ=255)
gATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑ccacca < 1:887944/76‑1 (MQ=255)
gATATCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑ccacca < 2:988119/76‑1 (MQ=255)
atatCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑ccaccca > 2:1068090/1‑74 (MQ=255)
atatCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACCG‑ccaccca > 1:1055507/1‑74 (MQ=255)
tatCGTGGCTCTCTTCACGCCACTGCTCGATCTTGCGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCaaa < 1:1942254/76‑1 (MQ=255)
tatCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCaaa < 2:476945/76‑1 (MQ=255)
atCGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAAc < 2:383978/76‑1 (MQ=255)
acngTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAAc > 2:1464089/4‑76 (MQ=255)
cGTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGc < 2:99782/76‑1 (MQ=255)
cGTGGCTCTCTTCACGCAACTGCTCGATCTTACGGCAGGCCTGAAGCACCGTCGTGGGGGCCCGGCCCACCaaagc > 2:1222127/1‑74 (MQ=255)
gTGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCa < 1:1390695/76‑1 (MQ=255)
tGGCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCAt > 1:1765348/1‑76 (MQ=255)
gCTCTCTTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCg < 2:907392/76‑1 (MQ=255)
ctctTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCGCCa > 1:34357/1‑76 (MQ=255)
ctctTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGGCACGG‑CCACCCAACGCATCGccc > 1:1231769/1‑75 (MQ=255)
ctTCACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCGCCAAt > 1:483791/1‑76 (MQ=255)
tanaCGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGGCACGG‑CCACCCAACGCATCGCCCAtc > 2:1466488/4‑76 (MQ=255)
cACGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGGGGGCACGG‑CCCCCCAAAGCAACGCCAAactc > 1:245240/1‑76 (MQ=255)
cGCCACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCGCCAATCTCCg < 2:1686497/76‑1 (MQ=255)
|
CATAGGTTTACGATGACAATGTTCTGATTAAATTTGAAAAATCTTCTTTGATATCGTGGCTCTCTTCACGCAACTGCTCGATCTTACGGCAGGCATGAAGCACCGTCGTGTGGTCACGG‑CCACCAAACGCATCGCCAATCTCCG > REL606/3842680‑3842823
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
