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 |
2,277,600 |
T→A |
47.5% |
S383S (TCA→TCT) |
btuB ← |
vitamin B12/cobalamin outer membrane transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,277,600 | 0 | T | A | 47.5%
| 4.0
/ 71.6
| 61 | S383S (TCA→TCT) | btuB | vitamin B12/cobalamin outer membrane transporter |
| Reads supporting (aligned to +/- strand): ref base T (9/23); new base A (7/22); total (16/45) |
| Fisher's exact test for biased strand distribution p-value = 7.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01 |
GCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGA > minE/2277537‑2277666
|
gCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGtt < 1:1156755/69‑1 (MQ=255)
gCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGtt < 1:2910390/69‑1 (MQ=255)
aTAACCTTCGATGAATTCCCAACCGGCTCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATc > 1:1156907/1‑69 (MQ=255)
aTAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGtt < 1:1718846/66‑1 (MQ=255)
aTAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATc > 1:2518156/1‑69 (MQ=255)
aTAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATc < 1:2015337/69‑1 (MQ=255)
taCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:175132/68‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:376700/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:3136614/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:189982/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:747021/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:1822995/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:176609/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:96220/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:2272650/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:1692704/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:2322560/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:163970/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:49696/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt < 1:515162/69‑1 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt > 1:1208041/1‑69 (MQ=255)
aaCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGt > 1:636213/1‑69 (MQ=255)
aCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGTc > 1:1841791/1‑69 (MQ=255)
aCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGTc > 1:2017643/1‑69 (MQ=255)
aCCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGTc > 1:807695/1‑69 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:315295/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:835301/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:3189382/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:994301/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2830014/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2805733/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:407345/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2677232/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:621038/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2675729/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2464005/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1518640/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1471330/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:142466/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1394548/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1302995/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1234133/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1224927/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:1899679/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:2136951/47‑1 (MQ=255)
gTTTGCCAGGTACCATGACGACCAAACTGAGAATTATCGTCGCTGCg < 1:220802/47‑1 (MQ=255)
ttCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACtt < 1:835398/69‑1 (MQ=255)
tCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACttg > 1:1716949/1‑69 (MQ=255)
tCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACtt < 1:361020/68‑1 (MQ=255)
ccATGACGACCAAACTGAGAATTATCTTCGCTGCg < 1:510142/35‑1 (MQ=19)
acgacCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAg > 1:2220327/1‑69 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:2652026/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:1140641/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:442789/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:358266/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:1898742/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCTGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTCGCTGCAg > 1:387305/1‑68 (MQ=255)
cgacCAAACTGAGAATTATCGTCGCAGCGTCCTGCGCCTTCAAAAGTAAAATCGCCGACTTGCTGCAg > 1:861381/1‑68 (MQ=255)
aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa < 1:1543739/69‑1 (MQ=255)
aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa < 1:416026/69‑1 (MQ=255)
aCTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCa < 1:323795/69‑1 (MQ=255)
tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga < 1:1669890/69‑1 (MQ=255)
tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga < 1:3300946/69‑1 (MQ=255)
tgtgAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCaga < 1:1835946/69‑1 (MQ=255)
|
GCGATAACCTTCGATGAATTCCCAACCGGCGCTGGTTTGCCAGGTTCCATGACGACCAAACTGTGAGTTATCGTCACTGCGTGCTGCGCCTTCAAAGGTAAAATCGCCGACTTGTTGCAGCCCGGTCAGA > minE/2277537‑2277666
|
| 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
