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 |
1,866,978 |
A→G |
58.6% |
Y125Y (TAT→TAC) |
ygcS ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,866,978 | 0 | A | G | 58.6%
| 12.9
/ 26.2
| 41 | Y125Y (TAT→TAC) | ygcS | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base A (6/11); new base G (15/9); total (21/20) |
| Fisher's exact test for biased strand distribution p-value = 1.18e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
TGCGCCCAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATAAGATGCTCTGGCG > minE/1866912‑1867036
|
tGCGCCCAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACGTACTGaata < 1:36284/69‑1 (MQ=255)
tGCGCCCAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGaata < 1:2798831/69‑1 (MQ=255)
cccAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATc < 1:853749/68‑1 (MQ=255)
cccAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATc < 1:2811866/68‑1 (MQ=255)
cccAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATc < 1:2638915/68‑1 (MQ=255)
aCCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGAcc < 1:948176/69‑1 (MQ=255)
ccGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGAcc < 1:826935/68‑1 (MQ=255)
ccGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCa > 1:3263341/1‑69 (MQ=255)
gcgcGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCaa < 1:918306/69‑1 (MQ=255)
gcgcGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCaa < 1:763999/69‑1 (MQ=255)
gcgcGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCaa < 1:2628499/69‑1 (MQ=255)
aTTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCATAcc < 1:2163560/46‑1 (MQ=255)
ccagcAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATaa < 1:2087004/69‑1 (MQ=255)
ccagcAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATaa < 1:2554001/69‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:3045009/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:3045742/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:127298/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:3333534/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:377890/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:969913/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:1219052/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:1946538/48‑1 (MQ=255)
cAAGGTGTGACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCaa < 1:2401428/48‑1 (MQ=255)
tgtgACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATAAGATGc > 1:2759461/1‑65 (MQ=255)
tgtgACCTACTGAATAATCGCCTCCCAGAACAATGCCAATCAAAATGCGCAGTCCAATAAGATGc > 1:355379/1‑65 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:2047434/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:1332504/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:1629384/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:1716159/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:1886477/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:736913/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:624562/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:398331/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:3025677/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:2685982/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:3303100/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:32124/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:31245/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:2929913/1‑69 (MQ=255)
gACCGACTGAGTAATCGCCTCCCAGACCAATGCCGATCAAAATGCGCAATCCAATAAGATGCTCTGGCg > 1:3040807/1‑69 (MQ=255)
aCCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATAAGATGCTCTGGCg > 1:753435/1‑68 (MQ=255)
aCCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATAAGATGCTCTGGCg > 1:2920595/1‑68 (MQ=255)
aCCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGACCAATAAGATGc > 1:766893/1‑61 (MQ=255)
|
TGCGCCCAGCAAAATACCGCGATGGCGGCGCGGGGAAAATTCAGCCAGCAAGGTGTGACCTACTGAATAATCGCCTCCCAGACCAATGCCAATCAAAATGCGCAGTCCAATAAGATGCTCTGGCG > minE/1866912‑1867036
|
| 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
