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 |
1,228,040 |
A→G |
100% |
I156I (ATT→ATC) |
yebZ ← |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,228,040 | 0 | A | G | 77.9%
| 71.9
/ 13.3
| 54 | I156I (ATT→ATC) | yebZ | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base A (6/6); new base G (42/0); total (48/6) |
| Fisher's exact test for biased strand distribution p-value = 3.58e-05 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCATACACCAGAGCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTACCCCTTCATTCAGCGTCGCA > minE/1227991‑1228103
|
gCATACACCAGAGCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGAt < 1:2867578/69‑1 (MQ=255)
gCATACACCAGAGCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGAt < 1:2809539/69‑1 (MQ=255)
cacCAGAGCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGt > 1:1672728/1‑68 (MQ=255)
agagCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGAt < 1:951497/60‑1 (MQ=255)
agCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATgg < 1:726966/69‑1 (MQ=255)
aGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGc > 1:2783190/1‑68 (MQ=255)
aGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCt > 1:322011/1‑69 (MQ=255)
aGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCt > 1:238528/1‑69 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:2303085/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:2317003/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:554611/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1958409/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:641029/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:2381401/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1692816/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1607770/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1528328/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1507870/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:2576011/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:906342/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1361801/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:1266456/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAGATCAGGTGa > 1:3049735/1‑35 (MQ=255)
aTCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTa > 1:2142872/1‑69 (MQ=255)
aTCCCCAAAACCACGCCGCCGCACAGATCAGGTGa > 1:750461/1‑35 (MQ=37)
ccccAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTAc < 1:1746118/67‑1 (MQ=255)
ccccAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTAc > 1:1350125/1‑67 (MQ=255)
ccccAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTAc < 1:988418/67‑1 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:3274164/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:3117263/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:3088244/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2372834/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:681573/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:3079915/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:833955/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:912195/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:920761/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2499283/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1153215/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1216701/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1367242/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1389540/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:140448/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:149958/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1578828/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1850900/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2188215/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2197423/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2246683/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:1020541/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2375165/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGAttt > 1:2801104/1‑40 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGATTTTCGCCGTTACCCCTTCATTCAACGTCGCa > 1:1057461/1‑69 (MQ=255)
gcACAGATCAGGTGAATTGCGTGATTAGTCTGATGGATTTTCGCCGTTACCCCTTCATTCAACGTCGCa > 1:1022571/1‑69 (MQ=255)
|
GCATACACCAGAGCACCGGCAGTAATCCCCCAAACCACGCCGCCGCACAAATCAGGTGAATCGCGTGATTAGTCTGATGGATTTTCGCTGTTACCCCTTCATTCAGCGTCGCA > minE/1227991‑1228103
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
