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 |
2,806,425 |
T→C |
37.4% |
S146S (AGT→AGC) |
tyrB → |
tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,806,425 | 0 | T | C | 37.4%
| 28.1
/ 33.8
| 56 | S146S (AGT→AGC) | tyrB | tyrosine aminotransferase, tyrosine‑repressible, PLP‑dependent |
| Reads supporting (aligned to +/- strand): ref base T (19/16); new base C (9/12); total (28/28) |
| Fisher's exact test for biased strand distribution p-value = 5.82e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.50e-01 |
TCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGACCTGTTGGCG > minE/2806358‑2806482
|
tCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:894472/69‑1 (MQ=255)
tCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:528087/69‑1 (MQ=255)
tCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:1553989/69‑1 (MQ=255)
tCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:231763/69‑1 (MQ=255)
tCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:3001543/69‑1 (MQ=255)
cTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTa < 1:427890/68‑1 (MQ=255)
gATCCTAGCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg < 1:730984/69‑1 (MQ=255)
gATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg < 1:1021908/69‑1 (MQ=255)
gATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg < 1:277413/69‑1 (MQ=255)
gATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg < 1:2938185/69‑1 (MQ=255)
gATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTAATTACCCCTgg < 1:241129/69‑1 (MQ=255)
ccTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg > 1:2711459/1‑66 (MQ=255)
ccTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg > 1:2776241/1‑66 (MQ=255)
aCCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGAc < 1:511721/69‑1 (MQ=255)
aCCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGAc < 1:3193182/69‑1 (MQ=255)
ttggAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:1738583/3‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTgg < 1:2656393/60‑1 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:2848129/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:3055536/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:1689581/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:331745/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:2413721/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGaa > 1:1175904/1‑69 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGTATGACGa > 1:111321/1‑68 (MQ=255)
tGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGCACTTACCCCTGGCATGACGaa > 1:1849866/1‑69 (MQ=255)
aCGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACg > 1:1599174/1‑69 (MQ=255)
aCGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACg > 1:510771/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:2476064/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:3396186/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:3404426/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:1458293/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:3022810/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:1394561/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:674502/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:1204368/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt > 1:2305922/1‑69 (MQ=255)
ttCGCCGGGGCTGGATTCGAAGTGAGTACTTACACCTGGTATGACGAAGCGACTAACGGCGTg > 1:1756630/1‑63 (MQ=255)
cGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATg < 1:3012622/68‑1 (MQ=255)
cGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATg < 1:481305/68‑1 (MQ=255)
ttCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGACCTGTTGGCg > 1:315680/1‑69 (MQ=255)
tCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGa > 1:630175/1‑58 (MQ=255)
tCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGa > 1:2762788/1‑58 (MQ=255)
tCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGa > 1:2816265/1‑58 (MQ=255)
tCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGa > 1:1883367/1‑58 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:161716/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:3246225/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:1737287/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:3111373/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:1741105/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:2951112/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:55823/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:1861203/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:1391085/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:837712/49‑1 (MQ=255)
aGTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:843049/49‑1 (MQ=255)
gTGAGCACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCttt < 1:3057369/48‑1 (MQ=255)
|
TCTGGGTCAGCGATCCTACCTGGGAAAACCACGTAGCAATATTCGCCGGGGCTGGATTCGAAGTGAGTACTTACCCCTGGTATGACGAAGCGACTAACGGCGTGCGCTTTAATGACCTGTTGGCG > minE/2806358‑2806482
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
