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 |
|
A10 F60 I1 R1
|
16 |
40.1 |
1364142 |
98.7% |
1346408 |
138.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,562,909 |
+CG |
coding (168/582 nt) |
ddpX ← |
D‑alanyl‑D‑alanine dipeptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,562,906 | 1 | . | G | 84.0%
| 76.4
/ 8.2
| 25 | coding (171/582 nt) | ddpX | D‑alanyl‑D‑alanine dipeptidase |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base G (11/10); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 5.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.40e-02 |
| * | NC_000913 | 1,562,906 | 2 | . | C | 84.0%
| 75.8
/ 8.2
| 25 | coding (171/582 nt) | ddpX | D‑alanyl‑D‑alanine dipeptidase |
| Reads supporting (aligned to +/- strand): ref base . (1/3); new base C (11/10); total (12/13) |
| Fisher's exact test for biased strand distribution p-value = 5.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.61e-02 |
CCGTGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCAGGCGTATTTCAATTCGATCTC > NC_000913/1562770‑1563025
||
ccGTGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCg < 1:166342/140‑1 (MQ=255)
gTGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCgcg < 2:11463/140‑3 (MQ=255)
tGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCgcga < 2:253637/140‑4 (MQ=255)
tGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCgcga > 1:253637/1‑137 (MQ=255)
tgATTAGAACCGACCGTCACA‑CAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACttt > 1:612382/1‑140 (MQ=255)
cgaccgTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAgcg < 1:412278/140‑1 (MQ=255)
cgaccgTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAgcg > 1:288836/1‑140 (MQ=255)
aacaTATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCtt < 2:444971/140‑1 (MQ=255)
tGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAAc > 1:52000/1‑140 (MQ=255)
cGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTgtgt < 1:413009/135‑1 (MQ=255)
cGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTgtgt > 2:413009/1‑135 (MQ=255)
ggTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGAc < 1:382810/140‑1 (MQ=255)
gTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCtt < 1:504782/128‑1 (MQ=255)
gTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCtt > 2:504782/1‑128 (MQ=255)
gTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACa > 1:208788/1‑140 (MQ=255)
gCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGc < 2:288836/140‑1 (MQ=255)
acaTCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAg > 1:71969/1‑140 (MQ=255)
tCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCtt < 2:612382/140‑1 (MQ=255)
tgtgCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCt < 2:52000/140‑1 (MQ=255)
gggCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCa > 1:672524/1‑140 (MQ=255)
aTACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCa > 1:54072/1‑140 (MQ=255)
aTACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCa > 2:471631/1‑140 (MQ=255)
aCCAGTTGTAACCCTGACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCAGGCGTATTTCAATTCg < 2:672524/140‑1 (MQ=255)
gACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCAGGCGTATTTCAATTCGAtctc > 2:187521/1‑130 (MQ=255)
gACAGCTGGGCGCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCAGGCGTATTTCAATTCGAtctc < 1:187521/130‑1 (MQ=255)
||
CCGTGCCACGGCTGTGATTAGAACCGACCGTCACATCAACAACATATTGCGGGTCTGGGCAGGCTTGCCACAACATCGCCTGTGCTTGTTGTGGGCGATACGCATCGTAAATCACCAGTTGTAACCCTGACAGCTGG‑‑GCGATGCTGATACTTTTCGCCAGCGCGGTAATCGCATCCTTGTGTAACAGACAACGCGCTTGCTGATAAATAGCTTTACCTGTGATGTTATCAGCGCAGGCGTATTTCAATTCGATCTC > NC_000913/1562770‑1563025
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
