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 |
|
A1 F71 I1 R1
|
21 |
57.4 |
2535598 |
87.8% |
2226255 |
142.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,196,220 |
C→T |
H366H (CAC→CAT) |
icd → |
isocitrate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,196,220 | 0 | C | T | 96.2%
| 55.7
/ NA
| 26 | H366H (CAC→CAT) | icd | isocitrate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (8/17); total (9/17) |
| Fisher's exact test for biased strand distribution p-value = 3.46e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGA > NC_000913/1196081‑1196315
|
tcggtatcgCCCCTGGTGCAAACATCGATGGCGAATTGGCTCTTTATGAAGCCACCCACGGTACTGCGCCTAAATATTCCGTTCATGACAAAGTAAATCCTCGCGCTATTATTCTCTCCTCTGAGACGATCCTGCGCCACAta > 2:1169912/1‑142 (MQ=255)
cgcgCCTGGTGCGAGCATCGGTGACGGATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGa < 2:922919/143‑1 (MQ=255)
cgCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGCGATGATGCTGCGCCATATGGGTTGGa < 2:751596/143‑1 (MQ=255)
cgCCCCTCGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGa < 2:1148147/143‑1 (MQ=255)
cccTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCCCTCCGCTGAGATGATGCTGCGCCATATGGGTCGGActg > 2:1225971/1‑141 (MQ=255)
tcccAAACACCGGTGACGACTGCGCTCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCg < 1:316962/140‑1 (MQ=255)
tGCTAACGTCGGGGACGAATGCGTCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTAGTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCgg < 2:839207/143‑1 (MQ=255)
tGCAAGTATCTGTGATGCATGCGCCCTGTTTGAAGCCACCCACTGTACTGCGCGGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCgg < 2:113009/143‑1 (MQ=255)
tcAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGc < 1:896383/142‑1 (MQ=255)
aaaCATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGAGTTGGACTGAAGCGGCTg > 1:527532/1‑143 (MQ=255)
aCATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAc > 1:213052/1‑143 (MQ=255)
ggTGACGAATGCGCCCTGTTTCAAGCCACTCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTACATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcctgat < 2:642960/143‑6 (MQ=38)
gTGACGAATGCGCCCTGTTTTAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGAtt < 2:1247051/143‑1 (MQ=38)
aTGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGTCGGTCAGGATAAAGTAAATGCTGGCTCTAGTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg < 1:56381/143‑1 (MQ=37)
gcCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATTCCGGTCAGTACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTAt < 1:54145/143‑1 (MQ=37)
tttGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCCGCTGACCTGATTGTTAAAGGTATGAAAgg > 2:832171/1‑143 (MQ=37)
tacacccacGGTTGTGCGCTGAAATGTCCCGGTCAGCACAAGGTAAAGCCTGGCTCTATGATGTGCGCCGCTGAGATGATCCTGTGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAAt < 2:301026/141‑1 (MQ=12)
acccacGGTACGGCGCCGTAATATGCCGGTCAGGACAAAGTAAATTCTTGCTCTATTTTTTTCTCCGCTGAGATGAAGCGGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa < 1:464758/143‑1 (MQ=18)
gcgcCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGt < 2:213052/143‑1 (MQ=18)
cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCACGACCGTAAcg > 2:125172/1‑142 (MQ=18)
aacatGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTTACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTAt < 2:630115/140‑1 (MQ=17)
ctccGGTCAGGACAAAGTAAATCATGGCTCTATTATTCTCTCCGCTGAGATGATTCTGTGTCATATTGTTTTAACTTAAGCGTCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACt < 1:230680/141‑1 (MQ=12)
gCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGATATGATTCTTCGCCATTTGGGTTGGAATGAAGAGGCTGACCTGAATGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACtt < 1:458038/143‑1 (MQ=14)
gACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGCTTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATAACAACGAACGTCt > 1:154872/1‑143 (MQ=14)
gACAAAGTAAATCCTGGCTCTATTATTCTCTCAGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCAAAGACCGTAACTTATGACTTCGaatgtgt > 2:637733/1‑137 (MQ=14)
gTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTCGAACGTCTgatgga > 1:1125630/1‑143 (MQ=11)
|
TCGGTATCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGA > NC_000913/1196081‑1196315
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
