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 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,187,809 |
A→G |
35.9% |
R16R (CGT→CGC) |
nanT ← |
sialic acid transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,187,809 | 0 | A | G | 35.9%
| 28.1
/ 27.9
| 50 | R16R (CGT→CGC) | nanT | sialic acid transporter |
| Reads supporting (aligned to +/- strand): ref base A (7/25); new base G (8/10); total (15/35) |
| Fisher's exact test for biased strand distribution p-value = 1.17e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAT > minE/2187744‑2187856
|
aaaaCGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACgg > 1:755855/1‑69 (MQ=255)
aaaaCGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACgg > 1:700019/1‑69 (MQ=255)
aaaaCGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACgg > 1:1407769/1‑69 (MQ=255)
aaaaCGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACgg > 1:524967/1‑69 (MQ=255)
aaaaCGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACgg > 1:319546/1‑69 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:185497/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:2346047/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:2675798/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:2790611/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:3049398/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:3342317/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:194453/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:2665236/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:238780/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:1611631/69‑1 (MQ=255)
cGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTga < 1:825191/69‑1 (MQ=255)
cAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGc < 1:1147196/69‑1 (MQ=255)
aaCCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGa < 1:1882090/68‑1 (MQ=255)
aaCCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGa < 1:3375760/68‑1 (MQ=255)
gATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGatat < 1:2626913/69‑1 (MQ=255)
gATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGatat < 1:2646313/69‑1 (MQ=255)
atCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCt > 1:130087/1‑69 (MQ=255)
atCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCt > 1:469169/1‑69 (MQ=255)
aCCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTg < 1:2038854/69‑1 (MQ=255)
ccAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATAGCACGGGATATTCTGGGTTgt < 1:588187/69‑1 (MQ=255)
aGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:844700/69‑1 (MQ=255)
aGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:1151458/69‑1 (MQ=255)
aGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:2286436/69‑1 (MQ=255)
aGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:3025876/69‑1 (MQ=255)
aGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:468024/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:2036585/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:97576/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:825250/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:1362843/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:1423826/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:1791290/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:2434710/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:2524875/69‑1 (MQ=255)
aGCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:2513549/69‑1 (MQ=255)
gCGGAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACt < 1:573486/68‑1 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCa > 1:972614/1‑68 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:2010899/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:2442623/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:3130235/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:294650/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:2342137/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:1127655/1‑69 (MQ=255)
ggAAAATGCCCGCCATTGTGCGCGGTTAAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAt > 1:2624744/1‑69 (MQ=255)
aaTGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGa < 1:277017/43‑1 (MQ=255)
aaTGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGa < 1:2386160/43‑1 (MQ=255)
|
AAAACGAAATCAAAACCGTCAAGCAGATATCCCAACCAGGCAGCGGAAAATGCGCGCCATTGTGCACGGTTGAGATGGCGATACCACGGGATATTCTGGGTTGTAGTACTCAT > minE/2187744‑2187856
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
