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 |
|
A4 F13 I0 R1
|
140 |
52.5 |
2164708 |
98.8% |
2138731 |
146.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947_CJ‑RC |
1,126,645:1 |
+C |
100% |
intergenic (‑99/+50) |
tdcG‑II ← / ← gcvP‑I |
L‑serine dehydratase/glycine dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947_CJ‑RC | 1,126,645 | 1 | . | C | 90.3%
| 23.9
/ ‑3.7
| 11 | intergenic (‑99/+50) | tdcG‑II/gcvP‑I | L‑serine dehydratase/glycine dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base . (1/0); major base C (6/3); minor base T (0/1); total (7/4) |
| Fisher's exact test for biased strand distribution p-value = 4.00e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.19e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑C‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGG > NC_002947_CJ‑RC/1126564‑1126781
|
ttgtggGGTGTACTTTGAGCCCGGTCGGCGGGGTTTTACCCGCTAAGGCGGTGTTATTGCCACCATCGCATTCGGGGTAAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATa < 2:179997/147‑1 (MQ=255)
cgGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCACGATCGACGGGCAGGCGCACACCAg > 8:84144/1‑147 (MQ=255)
ttttACCCGCGATTGCGGAGTTATAGCCACCATCGCATTGGGGGTTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGtt < 8:77805/146‑1 (MQ=255)
ttACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGc > 1:135649/1‑147 (MQ=255)
ccGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTc > 8:244221/1‑147 (MQ=255)
cgcgAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCg > 1:243456/1‑147 (MQ=255)
aaTGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑CACGCTCCAACACAGAGCCCGCCCCCCACCACACGAGGCGGGGAGGGCTATCAGCCGTCCTGATAGCTCACGATCGCCGGGCAGGCGCACACCAGGTTGAGGTCGCCg > 3:64206/1‑146 (MQ=255)
aTGCGGAGGTATAGCCACCATCGCATTCGCGGTAAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGaa < 6:109187/147‑1 (MQ=255)
tGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAac > 5:251878/1‑147 (MQ=255)
gcgGGTAAATC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcgg < 1:71706/146‑1 (MQ=255)
cgGGTAAACC‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACcggcgg > 8:254045/1‑145 (MQ=255)
|
TTGTTGGGTGGACATTGAGCCCTGTAGGCGCGGGTTTACCCGCGAATGCGGAGGTATAGCCACCATCGCATTCGCGGGTAAA‑C‑CGCTCCTACACAGAGCCCGCCACCCAAGCCAGGTGGCGGGGAGGGCTATCAGGCGTCCTGATAGCTCTCGATCGACGGGCAGGCGCACACCAGGTTGCGGTCGCCGAACACGTTGTCGACCCGGCCGACCGGCGG > NC_002947_CJ‑RC/1126564‑1126781
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
