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 F28 I1 R1
|
228 |
65.7 |
2434974 |
91.7% |
2232871 |
138.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,904,787 |
(T)7→8 |
intergenic (+41/‑14) |
manZ → / → yobD |
mannose‑specific PTS enzyme IID component/conserved inner membrane protein YobD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,904,780 | 1 | . | T | 97.4%
| 129.2
/ ‑3.5
| 38 | intergenic (+34/‑21) | manZ/yobD | mannose‑specific PTS enzyme IID component/conserved inner membrane protein YobD |
| Reads supporting (aligned to +/- strand): ref base . (0/1); new base T (17/20); total (17/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 |
TGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑G‑TTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAACGGCCCCACCCTGC > NC_000913/1904649‑1904903
|
tgtgGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑G‑tttttttt < 1:319298/140‑2 (MQ=255)
gtgGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑G‑tttttttta < 2:520211/140‑3 (MQ=255)
tACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTgg < 1:135256/140‑1 (MQ=255)
tACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTgg < 2:271751/140‑1 (MQ=255)
aCTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTgga < 2:421636/140‑1 (MQ=255)
tGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTggagg > 2:1185553/1‑140 (MQ=255)
gcgcAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTggagga > 1:982014/1‑140 (MQ=255)
gcgcAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTggagga < 1:959378/140‑1 (MQ=255)
aaGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGAc < 2:660313/140‑1 (MQ=255)
cTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGAcc < 1:793856/140‑1 (MQ=255)
atcatcGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTAc < 2:633767/140‑1 (MQ=255)
atcatcGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTAc < 2:445527/140‑1 (MQ=255)
atcGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGATGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGa > 1:1062345/1‑140 (MQ=255)
ggCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGt > 1:260388/1‑129 (MQ=255)
ggCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGt < 2:260388/129‑1 (MQ=255)
tcttcGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCAt < 1:1109847/140‑1 (MQ=255)
tcttcGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCAt < 2:550823/140‑1 (MQ=255)
ttcGTCATCGGTATAGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATcg > 2:534684/1‑140 (MQ=255)
gTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATcgccg < 2:982014/140‑1 (MQ=255)
gTCATCGGTATAGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATcgccg < 1:534684/140‑1 (MQ=255)
cGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTc > 2:666788/1‑140 (MQ=255)
gTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCt > 1:684923/1‑140 (MQ=255)
gTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCt < 1:666788/140‑1 (MQ=255)
gCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCt > 2:722512/1‑140 (MQ=255)
tGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCTCTCCTGGCCTTc < 2:834275/140‑1 (MQ=255)
ggTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcg < 1:152620/140‑1 (MQ=255)
tttccGCTTGCGCCTTGTGGGGATTTTAAGCCTTTTTTCCACTCCGGGGGCT‑TTTTGCCCC‑CTTT‑TTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcg < 2:1190236/136‑1 (MQ=255)
gTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGTGGATTAATGACAATCACGCACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcgc < 2:1084271/140‑1 (MQ=255)
gTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcgc < 1:86771/140‑1 (MQ=255)
gTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcgc < 2:30583/140‑1 (MQ=255)
gTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcgc < 2:184361/140‑1 (MQ=255)
cGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcg > 1:628380/1‑129 (MQ=255)
cGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTcg < 2:628380/129‑1 (MQ=255)
cGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGAt > 1:295072/1‑140 (MQ=255)
cGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGAt > 2:267889/1‑140 (MQ=255)
tgctgGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGtt > 1:1175258/1‑140 (MQ=255)
ttgGGACTGTAAGACTGTTGTGCTCTACCGGGCCC‑TTTTGGCCC‑CT‑T‑TTTTTTTATTGGGAGGATTAATGACAATCACGGACCTGCTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTtca < 2:867150/139‑1 (MQ=255)
aaGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCccg > 2:52575/1‑140 (MQ=255)
ttgtACACTACCGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAAc > 1:644579/1‑140 (MQ=255)
ctgcGGGGCCTTTTTGGCCCTT‑‑T‑TTTTTTTATCGGGAGGATTAATAAAAACCCGGGACGTGGTTGTTTTTTTTTCCACCCCCGCCCCCGTGCCCTCCGGTATCTACGATCATTTCCTCTGCCCCCGCCGTAACGGCCCCa < 2:428449/137‑1 (MQ=255)
ccGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAACGGCCCCAccc > 1:428449/1‑140 (MQ=255)
ccGGGGCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAACGGCCCCAccc > 2:140567/1‑140 (MQ=255)
gggCC‑TTTTGGCCC‑C‑‑GTTTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAACGGCCCCACCctgc > 1:382993/1‑140 (MQ=255)
|
TGTGGCTACTGCGCAAAAAAGTTAACCCGCTGTGGATCATCGTTGGCTTCTTCGTCATCGGTATCGCTGGTTACGCTTGCGGCCTGCTGGGACTGTAAGACTGTTGTACACTACCGGGGCC‑TTTTGGCCC‑C‑‑G‑TTTTTTTATCTGGAGGATTAATGACAATCACGGACCTGGTACTGATTCTTTTCATCGCCGCACTCCTGGCCTTCGCGATCTACGATCAGTTCATCATGCCCCGCCGTAACGGCCCCACCCTGC > NC_000913/1904649‑1904903
|
| 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
