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 |
|
A14 F1 I1 R1
|
71 |
51.6 |
2219666 |
95.9% |
2128659 |
118.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,632,151 |
T→C |
pseudogene (135/1284 nt) |
ydfJ ← |
pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,632,151 | 0 | T | C | 98.0%
| 186.8
/ NA
| 51 | pseudogene (135/1284 nt) | ydfJ | pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (28/22); minor base A (1/0); total (29/22) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCTCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATA > NC_000913/1632017‑1632286
|
ggTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGa < 1:1050001/139‑1 (MQ=255)
gCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAATGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACaa > 1:784340/1‑139 (MQ=255)
gCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACaa > 1:679725/1‑139 (MQ=255)
acCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGcc > 2:732949/1‑139 (MQ=255)
cAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCcac < 2:679725/139‑1 (MQ=255)
aTCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACAt < 1:853883/139‑1 (MQ=255)
gCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATAcg < 2:407711/125‑1 (MQ=255)
gCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATAcg > 1:407711/1‑125 (MQ=255)
tAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCAc < 1:528866/139‑1 (MQ=255)
gTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGt > 1:131798/1‑139 (MQ=255)
ggTAACACACCAATTAATGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTATGCCCTCTTCTGTCGCCCATTTTGCCTATAATAAATGTCACGACAATAGCCGCCACATAGCCTGCACCGTAgg > 1:425982/1‑139 (MQ=255)
ggTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCACCGACAATACGCGCCACATAACCTGCACCGTAgg > 1:786819/1‑139 (MQ=255)
cacCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCAt > 1:970484/1‑139 (MQ=255)
acCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCAtt > 1:293410/1‑139 (MQ=255)
aTTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCa < 2:703767/139‑1 (MQ=255)
aTTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCa > 1:805517/1‑139 (MQ=255)
aCAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGcc > 2:174753/1‑139 (MQ=255)
aTCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTg < 2:1063662/139‑1 (MQ=255)
aTCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTg > 2:518257/1‑139 (MQ=255)
aTCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTg < 2:1057689/139‑1 (MQ=255)
tCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCt > 1:975858/1‑101 (MQ=255)
tCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCt < 2:975858/101‑1 (MQ=255)
tcatGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTtga > 1:276445/1‑139 (MQ=255)
tGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTtgatga > 1:238723/1‑139 (MQ=255)
ggTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGc > 2:355437/1‑111 (MQ=255)
ggTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGc < 1:355437/111‑1 (MQ=255)
aTGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAg > 1:969334/1‑139 (MQ=255)
aataaAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGaaaa < 2:293410/139‑1 (MQ=255)
agCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCG‑AAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTcc < 2:463519/88‑1 (MQ=255)
agCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCG‑AAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTcc > 1:463519/1‑88 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATAcgc < 1:255936/61‑1 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATAcgc > 2:255936/1‑61 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGAtt < 2:460553/122‑1 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGAtt > 1:460553/1‑122 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCa > 1:985373/1‑139 (MQ=255)
cACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCa > 2:651203/1‑139 (MQ=255)
ttttttACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGa < 2:985373/139‑1 (MQ=255)
ttttttACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGa < 2:131798/139‑1 (MQ=255)
tttACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAac > 1:951440/1‑139 (MQ=255)
tACGCCCTATTCTGTCGCCCATTTTGCCGAAGATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCa > 2:422871/1‑99 (MQ=255)
tACGCCCTATTCTGTCGCCCATTTTGCCGAAGATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCa < 1:422871/99‑1 (MQ=255)
ccTATTCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACg > 2:453041/1‑139 (MQ=255)
ttCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACgcgc < 2:691954/46‑1 (MQ=255)
ttCTGTCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACgcgc > 1:691954/1‑46 (MQ=255)
tCGCCCATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGa > 1:933378/1‑139 (MQ=255)
cATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGAtt < 2:481770/95‑1 (MQ=255)
cATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGAtt > 1:481770/1‑95 (MQ=255)
cATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGa < 2:1059346/115‑1 (MQ=255)
cATTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGa > 1:1059346/1‑115 (MQ=255)
aTTTTGCCGAAAATAAATGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAat < 2:933378/139‑1 (MQ=255)
tGCCCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATa < 2:840695/139‑1 (MQ=255)
|
GGTGCAAAAACACCAATCTGTGCATAGGTCGGTAACACACCAATTAAGGTGGTACAGATCCCCATCATGGTGATGGTAATAAAGAGCACTTTTTTACGCCCTATTCTGTCGCCCATTTTGCCGAAAATAAATGCTCCGACAATACGCGCCACATAACCTGCACCGTAGGTTCCCATTGCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATA > NC_000913/1632017‑1632286
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
