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 |
2,008,326 |
G→A |
100% |
C232C (TGC→TGT) |
hybO ← |
hydrogenase 2, small subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,008,326 | 0 | G | A | 81.7%
| 54.8
/ 5.4
| 38 | C232C (TGC→TGT) | hybO | hydrogenase 2, small subunit |
| Reads supporting (aligned to +/- strand): ref base G (6/1); new base A (15/16); total (21/17) |
| Fisher's exact test for biased strand distribution p-value = 1.04e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TCATCACCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGACGGCCATAGGCGAAGGTCGGACGGTTTTTGTC > minE/2008273‑2008376
|
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2200853/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:3418798/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:356216/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:447611/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2955458/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2618627/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2584995/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2287363/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2057804/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2053902/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:601788/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:2005836/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:1783154/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:669552/69‑1 (MQ=255)
tcatcaCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:1779154/69‑1 (MQ=255)
caCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGAc > 1:214639/1‑69 (MQ=255)
caCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGAc > 1:2220673/1‑69 (MQ=255)
caCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGAc > 1:611397/1‑69 (MQ=255)
caCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGAc > 1:1635985/1‑69 (MQ=255)
aCCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGACg > 1:2707066/1‑69 (MQ=255)
aaCTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGACGGCCa < 1:454048/69‑1 (MQ=255)
ctctTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGACGGCCAt > 1:530328/1‑68 (MQ=255)
aaaCGACCAGCATCGAAGTGCGGGCGACGTTCACAGTGTTCGTGAATc < 1:1170212/48‑1 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGt > 1:2509324/1‑68 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:474994/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:514692/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:1022966/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:844139/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:3248583/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:3182209/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:2956789/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:2525967/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:249643/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:2113292/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:1918635/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTCGGACGGTTTTTGTc > 1:1262780/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGTGTTCGTGAATCAGACGACCATAGGCGAAAGTAGGACGGTTTTTGTc > 1:14325/1‑69 (MQ=255)
gAAGTGCGGGCGACGTTCACAGGGTTCGTGAATCAGACGACCATAGGCGAAAGTCgg > 1:1378699/1‑57 (MQ=255)
|
TCATCACCGAACTCTTTGGCAAAACGACCAGCATCGAAGTGCGGGCGACGTTCGCAGTGTTCGTGAATCAGACGGCCATAGGCGAAGGTCGGACGGTTTTTGTC > minE/2008273‑2008376
|
| 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
