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 |
1,156,766 |
A→G |
41.9% |
G220G (GGT→GGC) |
astD ← |
succinylglutamic semialdehyde dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,156,766 | 0 | A | G | 41.9%
| 17.2
/ 44.8
| 62 | G220G (GGT→GGC) | astD | succinylglutamic semialdehyde dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base A (16/20); new base G (12/14); total (28/34) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.41e-01 |
TCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTCACGCCC > minE/1156698‑1156828
|
tcAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTa > 1:3044311/1‑69 (MQ=255)
tcAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTa > 1:1846618/1‑69 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:1141960/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:2816779/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:2976295/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:29931/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:218615/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:1979074/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:3429695/69‑1 (MQ=255)
gCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:1264815/69‑1 (MQ=255)
cGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:897004/68‑1 (MQ=255)
cGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTa < 1:1873004/68‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:1585686/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2984110/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:1341658/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2182781/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2149691/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2123020/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2101168/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2056916/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:2053038/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:1364929/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:3239420/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:600942/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:696457/69‑1 (MQ=255)
agaATTTTCTCCGGCTGACCGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAAc < 1:341402/69‑1 (MQ=255)
ttttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa > 1:1654251/1‑69 (MQ=255)
tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCaa < 1:3255002/69‑1 (MQ=255)
tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa < 1:2838037/68‑1 (MQ=255)
tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa < 1:2889671/68‑1 (MQ=255)
tttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCa < 1:262556/68‑1 (MQ=255)
ttCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCaaa > 1:1303754/1‑69 (MQ=255)
tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTTTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga < 1:1942759/69‑1 (MQ=255)
tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga < 1:3145888/69‑1 (MQ=255)
tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga < 1:2493957/69‑1 (MQ=255)
tGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCgaga < 1:3375486/69‑1 (MQ=255)
gACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCTCTACCGGTAAACAGCAAACCGTCgaga < 1:780244/68‑1 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:3334779/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:3254600/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:3125445/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:927418/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:2724894/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:1557868/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:1714821/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:1367178/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:1355029/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:1927370/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:2339395/1‑64 (MQ=255)
cGGAAAGCTGGCGATGCAGCTGGTAGCCGGTATTGGCGCTGCCGGTAAACAGCAAGCCATCgag > 1:2544320/1‑64 (MQ=255)
cAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAgcgc > 1:2003896/1‑69 (MQ=255)
cAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAgcgc > 1:1858909/1‑69 (MQ=255)
cAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAgcgc > 1:1718775/1‑69 (MQ=255)
cAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAgcgc > 1:335400/1‑69 (MQ=255)
cAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAgcgc > 1:1586423/1‑69 (MQ=255)
aGCCTGTATTGGCGCTACCGGTAAACAGCAAGCCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCg > 1:1087134/1‑69 (MQ=255)
aGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCg > 1:6242/1‑69 (MQ=255)
cTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGttt > 1:2422279/1‑69 (MQ=255)
cTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGttt < 1:2576649/69‑1 (MQ=255)
cTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGttt > 1:152440/1‑69 (MQ=255)
tGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGttt > 1:2708573/1‑68 (MQ=255)
tGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTc > 1:186711/1‑69 (MQ=255)
ggCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTCAcgccc > 1:1636431/1‑69 (MQ=255)
ggCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTCAcgccc > 1:1818680/1‑69 (MQ=255)
ggCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTCAcgccc > 1:3090926/1‑69 (MQ=255)
|
TCAAGGGCGAGAATTTTCTCCGGCTGACCGGAGAGCTGGCGATGCAACTGGTAGCCTGTATTGGCGCTACCGGTAAACAGCAAACCGTCGAGATCCTCCAGCGCACTCAGCGCCTGACCCGTTTCACGCCC > minE/1156698‑1156828
|
| 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
