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 |
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 | 90.6%
| 104.0
/ 4.2
| 32 | coding (500/732 nt) | yfiH | UPF0124 family protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base C (11/18); total (13/19) |
| Fisher's exact test for biased strand distribution p-value = 5.52e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCC > NC_000913/2734414‑2734655
|
aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGTACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGaa < 2:10018/139‑1 (MQ=255)
aaCACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGaa < 2:1104309/139‑1 (MQ=255)
gCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCa > 1:256593/1‑139 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:898534/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 1:209986/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:598154/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:304241/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:256593/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATACTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:307803/139‑1 (MQ=255)
gCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc < 2:393331/139‑1 (MQ=255)
aaTATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAat < 2:859368/139‑1 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCGCTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCCTGGACCAATTGCCGGCCCTAACACGGCGAGAATATTTTcc > 1:445903/1‑139 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCg > 2:563412/1‑139 (MQ=255)
ccAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 1:190227/110‑1 (MQ=255)
ccAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc > 2:190227/1‑110 (MQ=255)
aTACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGAtt > 2:158774/1‑139 (MQ=255)
aCTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTAt < 2:437771/139‑1 (MQ=255)
tGCTGAATGGAAGCTGCACTTGCTTTAGCGTCTACTGTCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACC‑GGCGAGAATATTTTCCGGATTATCAGCAAAACAgg > 2:124213/1‑139 (MQ=255)
tGCTGAATGAAAGCTGCGCTTGCTGTAGCGTCTACTGCTGTAGACGACTCGCGTACCT‑CCGCCCCCTACTTCGAACACCCGTGGGCCACTTGCCGTCCCTATCCAGGCCAGCATGCTTCACGGGTTCTCAGGAAAACac > 1:156666/1‑138 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc > 1:489230/1‑93 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:489230/93‑1 (MQ=255)
ttGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 2:521614/139‑1 (MQ=255)
cGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:563412/139‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGcaca < 1:158774/139‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:863009/139‑1 (MQ=255)
cTACTGCCATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGcaca > 1:446943/1‑139 (MQ=255)
cATAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGCGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACg > 2:741600/1‑139 (MQ=255)
aTAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc > 1:1078241/1‑139 (MQ=255)
aTAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACgc < 2:793926/139‑1 (MQ=255)
tAAACGCCTCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAAAGGAAACCGTCCCTTCCAGCACGCCTGCGCACAGTCCACgcc > 1:916539/1‑139 (MQ=255)
tCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg < 2:39095/59‑1 (MQ=255)
tCGCGAACCTCCC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg > 1:39095/1‑59 (MQ=255)
|
AACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑CC‑CCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCC > NC_000913/2734414‑2734655
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
