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 |
|
A4 F1 I1 R1
|
765 |
39.6 |
1867486 |
94.4% |
1762906 |
108.0 |
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 | 88.0%
| 75.6
/ 4.0
| 25 | coding (500/732 nt) | yfiH | UPF0124 family protein |
| Reads supporting (aligned to +/- strand): ref base . (1/2); new base C (12/10); total (13/12) |
| Fisher's exact test for biased strand distribution p-value = 5.93e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATG > NC_000913/2734401‑2734665
|
cgAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑cccc < 1:91964/139‑1 (MQ=255)
aCGCTGCCGGGCAAGCCGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGGCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGc < 1:373517/139‑1 (MQ=255)
tctggcggATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATAttt > 2:371208/8‑139 (MQ=255)
ccGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGaa > 2:781186/1‑95 (MQ=255)
ccGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGaa < 1:781186/95‑1 (MQ=255)
cGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGGCTCGCGAACCGC‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTc < 1:167833/139‑1 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTcc > 1:761704/1‑139 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑cccccc > 2:712981/1‑82 (MQ=255)
gCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑cccccc < 1:712981/82‑1 (MQ=255)
tCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa < 1:463295/139‑1 (MQ=255)
cATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAAc > 1:124682/1‑139 (MQ=255)
aaGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa > 1:606223/1‑123 (MQ=255)
aaGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCa < 2:606223/123‑1 (MQ=255)
aGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGtctc > 1:927179/1‑139 (MQ=255)
cGTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAACAAAACAGGAAACCGTCTCTTCCAGCACGCCTgcgc > 1:439507/1‑139 (MQ=255)
gTCTACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 2:927179/139‑1 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCgaga > 2:382889/1‑80 (MQ=255)
tACTGCCATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCgaga < 1:382889/80‑1 (MQ=255)
ccATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa < 2:516972/106‑1 (MQ=255)
ccATAAACGCCTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGaaa > 1:516972/1‑106 (MQ=255)
cTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc > 1:646417/1‑51 (MQ=255)
cTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGcc < 2:646417/51‑1 (MQ=255)
cTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca < 1:816426/121‑1 (MQ=255)
cTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGca > 2:816426/1‑121 (MQ=255)
cTCGCGAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCcagccagc > 2:7763/1‑139 (MQ=255)
cTCGCGAACC‑T‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACg < 2:148309/112‑1 (MQ=255)
cTCGCGAACC‑T‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACg > 1:148309/1‑112 (MQ=255)
gcgAACC‑TCCCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATg < 2:439507/139‑1 (MQ=255)
|
CGAAAATTTGCTCAACACCCACGTTCGCCAGACGCTGCCGGGCAAGCTGATAAATATCCGCCAGATACTTATCACCATGCTGAATGAAAGCTGCACTTGCTTTAGCGTCTACTGCCATAAACGCCTCGCGAACC‑T‑CCCCCCCCACTTCGAACGCGCGTGGACCAATTGCCGGCCCTAACCAGGCGAGAATATTTTCCGGATTATCAGCAAAACAGGAAACCGTCTCTTCCAGCACGCCTGCGCACAGTCCACGCCAGCCAGCATG > NC_000913/2734401‑2734665
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
