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 |
|
A4 F1 I2 R1
|
67 |
32.5 |
1435938 |
95.9% |
1377064 |
112.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,288,561 |
(C)7→8 |
pseudogene (354/2525 nt) |
yejO ← |
pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,288,554 | 1 | . | C | 81.6%
| 109.8
/ 20.0
| 38 | pseudogene (361/2525 nt) | yejO | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| Reads supporting (aligned to +/- strand): ref base . (4/3); new base C (15/16); total (19/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.71e-01 |
CCGAGACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGAT > NC_000913/2288416‑2288683
|
ccGAGACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACg‑g > 1:196006/1‑139 (MQ=255)
cGAGACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCTCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑c < 2:223145/139‑1 (MQ=255)
tttGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑c‑ccccccca > 1:231878/1‑137 (MQ=255)
aaTACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCaa > 2:604824/1‑139 (MQ=255)
ccATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTaa > 2:56542/1‑139 (MQ=255)
gcgTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGcgcccgc > 1:140285/1‑139 (MQ=255)
tttAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGt < 1:595027/139‑1 (MQ=255)
aTAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTa > 2:228527/1‑139 (MQ=255)
aTAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATc < 2:547867/132‑1 (MQ=255)
aTAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATc > 1:547867/1‑132 (MQ=255)
ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGAtt < 1:219935/106‑1 (MQ=255)
ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGAtt > 2:219935/1‑106 (MQ=255)
ccTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCt > 2:716589/1‑139 (MQ=255)
tCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCAt < 2:140285/139‑1 (MQ=255)
aTCTACCGCAAATACAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAAc < 2:369961/139‑1 (MQ=255)
tACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGcgcc > 2:517401/1‑99 (MQ=255)
tACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGcgcc < 1:517401/99‑1 (MQ=255)
cGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCACCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAg > 1:579586/1‑139 (MQ=255)
caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 1:716589/139‑1 (MQ=255)
caaatgcaaatCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 2:484775/139‑1 (MQ=255)
cccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGc < 1:229348/139‑1 (MQ=255)
ccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGc > 1:78853/1‑104 (MQ=255)
ccTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGc < 2:78853/104‑1 (MQ=255)
tctTTTTCCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAATACG‑G‑CTCCCCCCATCTTTTTCAACTATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTa < 2:365016/139‑1 (MQ=255)
tAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAAt > 2:8593/1‑83 (MQ=255)
tAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAAt < 1:8593/83‑1 (MQ=255)
cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCa > 2:383733/1‑98 (MQ=255)
cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCa < 1:383733/98‑1 (MQ=255)
cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca > 2:401703/1‑111 (MQ=255)
cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 1:401703/111‑1 (MQ=255)
cAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGc > 2:397228/1‑139 (MQ=255)
agtagtCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAAcc > 1:317319/1‑102 (MQ=255)
agtagtCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAAcc < 2:317319/102‑1 (MQ=255)
agtCCTCCCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCcgcg < 2:231878/139‑1 (MQ=255)
tcctccCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGa < 1:534730/117‑1 (MQ=255)
tcctccCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGa > 2:534730/1‑117 (MQ=255)
ctccCTTTTCGATAGCGACAAAGATG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCAc > 2:222206/1‑139 (MQ=255)
ctccCTTTTCGATAGCGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCAc > 1:224646/1‑139 (MQ=255)
ttCGATAGCGACAAAGATG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTg < 1:222206/139‑1 (MQ=255)
cGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca > 1:492375/1‑88 (MQ=255)
cGACAAAGACG‑GCC‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGca < 2:492375/88‑1 (MQ=255)
cAAAGACGCC‑C‑CCCCCCATCTTTTGCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGAt < 2:579586/139‑1 (MQ=255)
|
CCGAGACGGTTTGTTCCGAATACCTCCATGGCCCGCGTGGTTGTTTTAATAGCACCGCCTGCTTTCTGATCTACCGCAAATGCAAATCCCCCCTCTTTAACCTCCAGTAGTCCTCCCTTTTCGATAGCGACAAAGACG‑G‑C‑CCCCCCATCTTTTTCAACGATTAAGCGCCCGCCTTTAATCGTGGTATCATTCGCTGCGCCATAAACCTGTAGCACACCATTATTGAGCGTAGTCTGGTTTGCCGCGCCACCCATTTGAACAATTTGAT > NC_000913/2288416‑2288683
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
