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 |
|
A13 F1 I1 R1
|
778 |
68.7 |
3228504 |
93.4% |
3015422 |
109.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,734,543 |
(C)8→9 |
coding (492/732 nt) |
yfiH ← |
UPF0124 family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,734,535 | 1 | . | C | 91.9%
| 118.6
/ 2.9
| 37 | coding (500/732 nt) | yfiH | UPF0124 family protein |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base C (20/14); total (21/16) |
| Fisher's exact test for biased strand distribution p-value = 5.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01 |
AATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGC > NC_000913/2734405‑2734662
|
aaTTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑‑cccccccc < 1:931029/139‑1 (MQ=255)
aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGaa < 2:316662/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:1449872/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCAGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCGC‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:1554310/139‑1 (MQ=255)
gCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc > 1:1587324/1‑139 (MQ=255)
tAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCgaga < 2:809710/139‑1 (MQ=255)
tCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc > 2:489680/1‑114 (MQ=255)
tCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 1:489680/114‑1 (MQ=255)
aCCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCaa < 2:1190786/139‑1 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGaa < 1:504711/77‑1 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGaa > 2:504711/1‑77 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc < 1:1525939/100‑1 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc > 2:1525939/1‑100 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc > 1:980822/1‑139 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAATACAgg > 1:744146/1‑139 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATAAGCAAAACAgg > 1:604977/1‑139 (MQ=255)
gaatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa > 2:359784/1‑139 (MQ=255)
gCTGCACTTGCTTTCGCGTCTACTGCCATAAACGCCTCGCCAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTctct > 2:979605/1‑139 (MQ=255)
gCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGGGAATATTTTCCGGATTATCAGCAAAGCAGGAAACCGTCTCTTcc > 2:1082079/1‑139 (MQ=255)
aCTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc > 1:501872/1‑76 (MQ=255)
aCTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:501872/76‑1 (MQ=255)
gCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACg > 1:1286900/1‑139 (MQ=255)
aGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa > 2:129168/1‑132 (MQ=255)
aGCGTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 1:129168/132‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 2:1527991/139‑1 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAg > 2:687309/1‑139 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAg > 2:1022199/1‑139 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑T‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg < 2:836992/98‑1 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑T‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg > 1:836992/1‑98 (MQ=255)
aCTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc < 2:152623/65‑1 (MQ=255)
aCTGCCATAAACGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc > 1:152623/1‑65 (MQ=255)
aaCGCCTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgccag < 2:980822/139‑1 (MQ=255)
cTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:1187140/46‑1 (MQ=255)
cTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc > 1:1187140/1‑46 (MQ=255)
cTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCcagccagc > 1:43531/1‑139 (MQ=255)
cTCGCGAACC‑TC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGACCACCCcagcccgc > 1:408648/1‑139 (MQ=255)
cgcgAACC‑TCCCCCCCCCCACTTCGAACGCGCGTGGACCAATTg > 1:988858/1‑44 (MQ=255)
cgcgAACC‑TCCCCCCCCCCACTTCGAACGCGCGTGGACCAATTg < 2:988858/44‑1 (MQ=255)
|
AATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGC > NC_000913/2734405‑2734662
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
