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 |
|
A8 F9 I0 R1
|
23 |
38.9 |
1378630 |
88.6% |
1221466 |
148.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913_3_hsa_tpiA |
2,795,396 |
C→A |
100% |
Q382K (CAG→AAG) |
gabP → |
gamma‑aminobutyrate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913_3_hsa_tpiA | 2,795,396 | 0 | C | A | 96.9%
| 85.4
/ ‑4.8
| 33 | Q382K (CAG→AAG) | gabP | gamma‑aminobutyrate transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (21/10); total (22/11) |
| Fisher's exact test for biased strand distribution p-value = 3.44e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGTACGTGGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAG > NC_000913_3_hsa_tpiA/2795253‑2795540
|
cGTACGTGGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGCAGGTATTTAAATTTCTGATCGACACCTCCGGCGCTATAGCCCTGCTGGTTTATTTAGTCATCGCGGTTTCAAAGttc > 2:275193/1‑148 (MQ=255)
gtTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATAGCCGTTTCAAAGTTCAGGAGTCGCaaaa > 1:96089/1‑149 (MQ=255)
gtTACTCTCCACCGGCGCGGCATTCGTAACGGTGGCGGTGAACGATTACGCGCCTGAGAAGGTATTTAACTTTCTGATCGACAGCTCCGGCGCTATCGCCCAGCTGGTTATTTTAGTCATCGCCGTTCCAGAGTTGCGGATGCGCaaaa > 1:520807/1‑149 (MQ=255)
tACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTCTTTAGTCATCGCCGTTTCCAAGTTGCGGATGCGCACAAtt > 1:442691/1‑149 (MQ=255)
ttAACGGTGGTGGTGAACTATTAGGGGCCTGCGGAGGTATTTAAATTTCTGATCGCCAGCTCTGGAGCTATGGCCCTGATGGTTTTTTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGAATACTTTTGCGAGCTGAAGGAAGGGAGAt > 2:158425/1‑149 (MQ=255)
aaCGGTGGTGGTTAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTc < 1:22372/149‑1 (MQ=255)
tggtggtgAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTg > 1:587063/1‑149 (MQ=255)
aaCTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCAGCGCTATCGCCCTGCTGGGTTATTTAGTCATCGACGTTTCAAAGATACGGATGTTCATAATTCAGCGTGCCGAAGGAAGCGAGATTCGCTTGCCGAtgtg > 2:38206/1‑149 (MQ=255)
tATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTCCGGGCAGAAGGAGGCAAAATTCGCTTGCGAATGTGGCt > 1:607933/1‑149 (MQ=255)
tATTACGCGCCTGCGAAGGTATTATAATTTTTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCt < 1:352531/149‑1 (MQ=255)
gtttACGCGTCTGCGAAGGGATGTATGTTTCTGAGTGAGAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGGCAACGCCGTTTTAAAGTTGCGGAGGCGCAAAATTCTGCAAGCAGAAGGAAGCGGTATTCGCTTGTGAATGTGGCt < 2:198791/147‑1 (MQ=255)
ttACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGCAGGAAGCGAAATTCGCTTGCGAATGTGGGttt > 2:546949/1‑149 (MQ=255)
ttACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCttt > 1:586719/1‑149 (MQ=255)
ttACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTCCGAATGTGGCttt > 2:333156/1‑149 (MQ=255)
gcgcCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATcc > 1:317410/1‑149 (MQ=255)
gcCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGGTGTGCGCTCATATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGt < 1:473210/149‑1 (MQ=255)
cTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTgg > 2:524337/1‑149 (MQ=255)
cGAAGGTATTTAACTTTCTGGTCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTGTTTTGTCATCCGCGTTTCACAGTTGCGGTTGCGCAAAATTCTGCGAGCAGAAGTAATCGAAATGCGCTTGCGAATGTGGCCTTATCCGTGGCTc < 2:353519/149‑1 (MQ=255)
ttAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTa < 1:576246/149‑1 (MQ=255)
tttCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTCGTCAt > 1:667521/1‑149 (MQ=255)
ttCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATc < 1:44474/149‑1 (MQ=255)
tGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGc > 2:181864/1‑149 (MQ=255)
gATCGACAGCTCCGGCGCTGTCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAGTTATGCGAGCAGAAGGAGGCGAAATGCGCTTGCGGATGTGGCTTTATCCTTGGCCCACCTAGCTAGCCATCGGCt > 2:416034/1‑149 (MQ=255)
tCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGCGTTTTTTACCtt > 2:191959/1‑149 (MQ=255)
ttCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGAGAAATTCGCTTGGGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGt < 1:216798/148‑1 (MQ=255)
cccTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGGGTTGGTAGTg > 1:541879/1‑149 (MQ=255)
ccTGCTGGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGa > 1:57543/1‑149 (MQ=255)
ctgGTTTATTTAGTCATCGCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTCTATTCCCTTTGTCTTGGTCGTGAGGCt > 2:213738/1‑149 (MQ=255)
tctaGCCAGCGCCGTTTCAAAGTTACGGATGCGCAAAATCTTTCCAACAGAAGGAAGCGAAACACGCCTGCGAATGTGCCGCTACCCGTGGCTCACCTGGCTAGTCAGCGGCTTAATTAACTCCAGGATGGTAGTGATGCTATtccgtc < 2:347641/147‑1 (MQ=255)
gCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa > 1:510368/1‑149 (MQ=255)
gCCGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACa > 1:320034/1‑149 (MQ=255)
cGTTTCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGt < 1:617044/149‑1 (MQ=255)
ttCAAAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAg < 1:555420/149‑1 (MQ=255)
|
CGTACGTGGCGGTGTTACTCTCCACCGGCGCGGCATTCTTAACGGTGGTGGTGAACTATTACGCGCCTGCGAAGGTATTTAAATTTCTGATCGACAGCTCCGGCGCTATCGCCCTGCTGGTTTATTTAGTCATCGCCGTTTCACAGTTGCGGATGCGCAAAATTCTGCGAGCAGAAGGAAGCGAAATTCGCTTGCGAATGTGGCTTTATCCGTGGCTCACCTGGCTAGTCATCGGCTTTATTACCTTTGTGTTGGTAGTGATGCTATTCCGTCCGGCGCAACAGTTAG > NC_000913_3_hsa_tpiA/2795253‑2795540
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
