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 |
|
A11 F142 I1 R1
|
99 |
64.8 |
3148104 |
96.3% |
3031624 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,950,467 |
2 bp→TT |
intergenic (+47/‑39) |
ilvL → / → ilvX |
ilvG operon leader peptide/uncharacterized protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,950,467 | 0 | G | T | 82.9%
| 89.1
/ 19.0
| 41 | intergenic (+47/‑40) | ilvL/ilvX | ilvG operon leader peptide/uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base G (2/5); new base T (17/17); total (19/22) |
| Fisher's exact test for biased strand distribution p-value = 4.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.04e-01 |
| * | NC_000913 | 3,950,468 | 0 | G | T | 97.5%
| 129.0
/ NA
| 41 | intergenic (+48/‑39) | ilvL/ilvX | ilvG operon leader peptide/uncharacterized protein |
| Reads supporting (aligned to +/- strand): ref base G (1/0); major base T (18/21); minor base C (0/1); total (19/22) |
| 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 |
TTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACT > NC_000913/3950377‑3950559
||
ttatCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGtttttttttt > 1:788979/1‑100 (MQ=255)
tatCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTg < 1:1425090/100‑1 (MQ=255)
tatCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTg < 1:572074/100‑1 (MQ=255)
atCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGa < 1:904942/100‑1 (MQ=255)
tCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGAc > 1:1356332/1‑100 (MQ=255)
tCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTCTGAc < 2:1197324/100‑1 (MQ=255)
cccACCGTGCGGGGCTGCACTTGGCCGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGCCCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGAcc < 1:266522/100‑1 (MQ=255)
cccACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGAcc < 1:287604/100‑1 (MQ=255)
cACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTTTCCtt > 2:1335598/1‑100 (MQ=255)
ggggggGTGGAATTGGACGAGGAAAGGCGTAGAGATCAAGTCTTAACGAACTAAGACCCCCGAACCGAAAGGTCCGGGTTTTTTTTTTGACCTTaaaaa < 2:1290463/97‑1 (MQ=255)
ggggGTGCACTTGGACGAGGACCGGCTGGGAGATCAAGCCTTAACGAACTAAGACCCCCAAAACGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACa < 2:382789/99‑1 (MQ=255)
ggggCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCC‑GGGTTTTTTTTTGACCTTAAAAACATa < 2:749334/100‑1 (MQ=255)
ggggCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCC‑GGGTTTTTTTTTGACCTTAAAAACATa < 2:748931/100‑1 (MQ=255)
tGCGCTTGGGCGAGGAAAGGCTCCGAGAGCGGGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCg < 2:982908/100‑1 (MQ=255)
cTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCgagg < 1:374584/99‑1 (MQ=255)
ggACGAGGATAGGCCTAGAGAGCGGGCCTTAACGAACAAAGACAACCGCACCGAAAGGACCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGc < 1:267486/99‑1 (MQ=255)
ggACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCC‑GGGTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAg > 1:511774/1‑100 (MQ=255)
gagggtgAAAGCCTTAGAGATCAAGCCTTATCGGACTAAGACACACACACAGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAg < 2:304944/94‑1 (MQ=255)
gACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAg > 1:1434390/1‑100 (MQ=255)
gACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAg > 1:859752/1‑100 (MQ=255)
gACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAg > 1:859840/1‑100 (MQ=255)
ggAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAAt > 2:164908/1‑100 (MQ=255)
cTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATaa > 2:1315835/1‑99 (MQ=255)
ttAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGAAAATGAATAACa > 1:319637/1‑100 (MQ=255)
gCCGTAATGAAGTACGCCCCCCGCTCCGAAAGGGCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACaa < 2:1222169/95‑1 (MQ=255)
ttAACGAGCTAAGACCCCCACACCGAAAGGGCCGGGTTTTTTTTTGGACCATAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTg < 2:732889/99‑1 (MQ=255)
tAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGtt > 2:1041317/1‑100 (MQ=255)
naCGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGttt > 1:690598/2‑100 (MQ=255)
cGAACTAAGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTtct > 1:963963/1‑100 (MQ=255)
aagtaggACCCCCGCACCGAAAGG‑GCGGGGTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCa < 2:791734/93‑1 (MQ=255)
aaGACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTTTTCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGAt > 2:1571933/1‑100 (MQ=255)
aGACCCCCGCACCGAAAGGGGC‑GGGTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTc < 1:935928/100‑1 (MQ=255)
gACCCCCGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTc > 1:572980/1‑100 (MQ=255)
cccccGCCCCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCa < 2:788974/99‑1 (MQ=255)
cccccGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAg > 1:851194/1‑100 (MQ=255)
ccccGCTCCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAgg < 2:572977/100‑1 (MQ=255)
ccGCACCGAAAGGTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGAc > 1:666593/1‑100 (MQ=255)
cACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAGCCGAGGAGCAGACAATGAAAAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACggg > 2:857725/1‑100 (MQ=255)
ccGAAAGGTCCGGGTTTTTTTTTTTAACTTAAAAAAATAACCACGGACCAGACAATCAATAACAGCACCAAAATCCTTTCCTCAAGCTTCAGGAc > 2:1431574/1‑95 (MQ=255)
cagAAGGGTCAGGGTCTGTTTGTTGGCCGTAAAAACATAAGCGAGGAGCAGACAATCAATAACAGCACAAAATTCTGTTTCTCAAGATTc < 2:297118/88‑1 (MQ=255)
gAAAGGTCC‑GGGTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaact < 2:1485186/100‑1 (MQ=255)
gTCCGGGTTTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaactaact > 1:1118311/1‑100 (MQ=255)
||
TTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGACCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAACTAACT > NC_000913/3950377‑3950559
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
