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 |
|
A2 F1 I1 R1
|
81 |
28.9 |
1316934 |
95.8% |
1261622 |
113.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
4,575,425 |
A→G |
pseudogene (1507/2937 nt) |
yjiV → |
pseudogene, conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 4,575,425 | 0 | A | G | 96.3%
| 88.9
/ ‑6.0
| 27 | pseudogene (1507/2937 nt) | yjiV | pseudogene, conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (0/1); new base G (10/16); total (10/17) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
GATCATTACGTTCGCGAGAGCAACTTCACACAGCTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACAGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGATATTATCAATACATGGC > NC_000913/4575299‑4575542
|
gATCATTACGTTCGCGAGAGCAACTTCACACAGCTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTc > 1:413543/1‑139 (MQ=255)
cgcgAGAGCAACTTCACACAGCTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATg > 2:192173/1‑139 (MQ=255)
cAACTTCACACAGCTGGATGATGAGCTGAAAAACTGTATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTa < 2:413543/139‑1 (MQ=255)
cTTCACACAGCTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATcc > 1:537659/1‑139 (MQ=255)
cTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAg > 2:441354/1‑139 (MQ=255)
cTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAg > 2:521528/1‑139 (MQ=255)
gatgatGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGa > 1:10366/1‑139 (MQ=255)
aGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCt > 1:199454/1‑139 (MQ=255)
aGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCt > 1:80021/1‑139 (MQ=255)
tGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTggggg < 1:441354/139‑1 (MQ=255)
gaatGGTAGCCGTTATTAATAAAAATTCGTCCGTAACCCGGAGTCAAAAGATCCTGACGATAATCGGAACGGACGCTGGTCTGAAAGTCGTAATGGCAACGTATCCGATCGTTTAGCGAAGTTGCTGATGCTGGGGGCt < 1:334806/136‑1 (MQ=255)
gATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCt < 1:192173/139‑1 (MQ=255)
ttGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCaa > 1:381439/1‑97 (MQ=255)
ttGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCaa < 2:381439/97‑1 (MQ=255)
aaTTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGc < 2:434282/139‑1 (MQ=255)
aaTTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGc < 2:655998/139‑1 (MQ=255)
cGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTg < 1:287738/139‑1 (MQ=255)
tAACCCGGAATCAAAATATCCGGAAGATAAGCAGAACAGACGCTGGCCTCAAATTCGTAATGGCTACGTATCCCAACGTTTAGCGAAGTTGCGAATGCTGGGGGCTGGATTCAAAACCGTCAATGCCGCAACTATTGat < 1:551474/139‑1 (MQ=255)
tAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGat < 2:199454/139‑1 (MQ=255)
tAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGat < 2:224068/139‑1 (MQ=255)
tAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGat < 1:521528/139‑1 (MQ=255)
cGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGAtattat < 2:80021/139‑1 (MQ=255)
cGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGAtattat < 2:388950/139‑1 (MQ=255)
cGGAATCAAAAGATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGAtattat < 2:321480/139‑1 (MQ=255)
gATCCTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGATATTATCAATACATGGc < 2:10366/139‑1 (MQ=255)
cTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCa > 2:499465/1‑55 (MQ=255)
cTGAAGATAATCAGAACGGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCa < 1:499465/55‑1 (MQ=255)
|
GATCATTACGTTCGCGAGAGCAACTTCACACAGCTGGATGATGAGCTGAAAAACTGGATTGGTAGCCGTTTTTCATCAAAATTCGTCCGTAACCCGGAATCAAAAGATCCTGAAGATAATCAGAACAGACGCTGGCCTCAAATTCGTAATGGCAACGTATCCCATCGTTTAGCGAAGTTGCTGATGCTGGGGGCTGGATTCAAAACCGTCAATGCGGCAACTATTGATATTATCAATACATGGC > NC_000913/4575299‑4575542
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
