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 |
|
A9 F1 I1 R1
|
64 |
69.7 |
3300380 |
93.4% |
3082554 |
111.2 |
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 | 89.7%
| 92.8
/ 4.0
| 29 | coding (500/732 nt) | yfiH | UPF0124 family protein |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base C (12/14); total (14/15) |
| Fisher's exact test for biased strand distribution p-value = 5.98e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01 |
AAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCA > NC_000913/2734403‑2734644
|
aaaaTTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑cccccc < 2:1323253/139‑1 (MQ=255)
aaTTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑cccccccc < 1:516024/139‑1 (MQ=255)
cACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAAcgcgcg < 1:339320/139‑1 (MQ=255)
aaGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCa < 2:1026261/139‑1 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc > 1:1055539/1‑139 (MQ=255)
tATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg < 2:1230096/139‑1 (MQ=255)
tATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg < 2:924815/139‑1 (MQ=255)
tATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGCCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg > 1:1211046/1‑139 (MQ=255)
tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg < 2:1198549/137‑1 (MQ=255)
tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg > 1:1198549/1‑137 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc > 1:310558/1‑139 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc < 1:628967/121‑1 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc > 2:628967/1‑121 (MQ=255)
tGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAg > 1:1377746/1‑139 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:700979/92‑1 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc > 1:700979/1‑92 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAgg > 2:610966/1‑139 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑cc < 1:1291813/59‑1 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑cc > 2:1291813/1‑59 (MQ=255)
gCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGa > 2:914004/1‑139 (MQ=255)
gaatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCCCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa < 2:1620442/139‑1 (MQ=255)
aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg < 2:1010086/102‑1 (MQ=255)
aatgaaAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAgg > 1:1010086/1‑102 (MQ=255)
ttGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 2:26052/139‑1 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 2:1377746/139‑1 (MQ=255)
aggacagCCATAAACCCCTCGCCAACCTCCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:1588117/133‑1 (MQ=255)
ccATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg > 2:1218851/1‑94 (MQ=255)
ccATAAACGCCTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAg < 1:1218851/94‑1 (MQ=255)
cTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg < 1:986379/109‑1 (MQ=255)
cTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAg > 2:986379/1‑109 (MQ=255)
cTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa < 2:502902/111‑1 (MQ=255)
cTCGCGAACCTC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCa > 1:502902/1‑111 (MQ=255)
cTCGCGAACCT‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 2:310298/45‑1 (MQ=255)
cTCGCGAACCT‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGc > 1:310298/1‑45 (MQ=255)
|
AAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACCT‑‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCA > NC_000913/2734403‑2734644
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
