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 |
|
A5 F28 I3 R1
|
375 |
42.1 |
2927644 |
71.4% |
2090337 |
57.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
635,229 |
G→A |
D188D (GAC→GAT) |
ybdN ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 635,229 | 0 | G | A | 77.8%
| 45.7
/ 9.7
| 27 | D188D (GAC→GAT) | ybdN | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (6/0); new base A (0/21); total (6/21) |
| Fisher's exact test for biased strand distribution p-value = 3.38e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01 |
AGTCCAGGGTTTATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAT > W3110S.gb/635214‑635287
|
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1823317/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2531425/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2536534/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:609675/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:618334/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:244807/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:651185/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2602856/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2819982/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2849119/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:836053/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1937299/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:2869465/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1571876/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1515885/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1393473/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:525781/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1374715/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1310366/62‑1 (MQ=255)
aGTCCAGGGCTTATCATCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:343244/62‑1 (MQ=255)
ccAGGGCTTATCATCTGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGt < 1:1182069/59‑1 (MQ=255)
tATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGt > 1:1686371/1‑54 (MQ=255)
tATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGt > 1:1782890/1‑54 (MQ=255)
tATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGt > 1:1473499/1‑54 (MQ=255)
tATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGt > 1:2106346/1‑54 (MQ=255)
tATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGt > 1:2586579/1‑54 (MQ=255)
tATCGTCGGCAAAAAGTTGTTTATTTAAACtggcgat > 1:1543856/1‑37 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:47422/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:40731/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2638681/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2819308/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2247087/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2480998/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2313019/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:821149/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2144995/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:905773/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:972634/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:106978/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:999734/61‑1 (MQ=255)
tcgtcgGCAAAACGTTGTTTATTCAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAt < 1:2087083/61‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCcaca < 1:2274339/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:2468152/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:842720/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:511647/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:471919/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:380144/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:2471442/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:1028932/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:2420170/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:2023587/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:1669664/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:130374/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:112675/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACa < 1:1063913/40‑1 (MQ=255)
gtcgGCAAAACGTTGTTTATTTAAACTG‑‑GATGGCGACa < 1:2293976/38‑1 (MQ=37)
|
AGTCCAGGGTTTATCGTCGGCAAAACGTTGTTTATTTAAACTGGCGATGGCGACAAAACGGTTGTAGGACTCAT > W3110S.gb/635214‑635287
|
| 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
