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 |
1,998,490 |
C→G |
39.5% |
L214L (CTG→CTC) |
pitB ← |
phosphate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,998,490 | 0 | C | G | 39.5%
| 27.7
/ 38.4
| 43 | L214L (CTG→CTC) | pitB | phosphate transporter |
| Reads supporting (aligned to +/- strand): ref base C (12/14); new base G (10/7); total (22/21) |
| Fisher's exact test for biased strand distribution p-value = 5.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01 |
ACCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGC > minE/1998422‑1998542
|
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:3316167/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2231221/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2279206/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2282193/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2295369/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc < 1:2369268/69‑1 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2531032/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2587935/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2749995/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:1050828/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:3430144/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:367360/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc < 1:475913/69‑1 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:650659/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:674035/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:754275/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:826355/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:1290524/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:2156921/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:1640451/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:1982461/1‑69 (MQ=255)
aCCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATc > 1:1148335/1‑69 (MQ=255)
cAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAg > 1:522478/1‑69 (MQ=255)
cAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAg > 1:2151911/1‑69 (MQ=255)
cAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAg > 1:2953284/1‑69 (MQ=255)
gCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAgcgc > 1:2960214/1‑69 (MQ=255)
gCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAgcgc > 1:1698060/1‑69 (MQ=255)
cGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCaa > 1:831638/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAGACAATCAGCGCAATAcg > 1:2785876/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATAcg > 1:2179093/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATAcg > 1:493239/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATAcg > 1:244049/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATAcg > 1:2181103/1‑69 (MQ=255)
cccTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATAcg > 1:3249519/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGGGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:1351463/1‑69 (MQ=18)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:3394559/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:2936003/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:52076/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:704279/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:2241868/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:2302244/1‑69 (MQ=255)
ccGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGAAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:2266275/1‑69 (MQ=18)
ccGTCGTTAGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:237072/1‑69 (MQ=18)
cagtcgtTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATGAGGGCAATACGCGTCCAGAAt > 1:1797109/3‑69 (MQ=18)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:2874076/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:701414/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:1203587/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:615517/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:1905483/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:1831949/69‑1 (MQ=255)
cccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTg < 1:2833990/69‑1 (MQ=255)
ccGCAGCGGTAACAATCAGCGCAATTCGCGTCCTGAATGGCGGTTTACGTTTGGCTTTTTTCTTTTTGc < 1:1264966/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:440552/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:255359/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:2601467/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:172770/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:2878336/69‑1 (MQ=255)
ccGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGc < 1:783059/69‑1 (MQ=255)
aaCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:460992/57‑1 (MQ=25)
aaCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:435874/57‑1 (MQ=25)
aaCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:2102705/57‑1 (MQ=25)
aaCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:2724645/57‑1 (MQ=25)
aCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:85764/56‑1 (MQ=25)
aCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:2035537/56‑1 (MQ=25)
aCAATGAGGGCAATACGCGTCCAGAATGGCGGCTTACGTTTGCCTTTTTTCttttt < 1:1120741/56‑1 (MQ=25)
|
ACCAGGCCGATCCCTTTTTGTCCGTCGTTCGCGCCGTGCGAAAACGCCACGCCCGCAGCGGAAACAATCAGCGCAATACGCGTCCAGAATGGCGGTTTACGTTTGCCTTTTTTCTTTTTGC > minE/1998422‑1998542
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
