Multi-Genome Alignment Report

Flow Cell ID:	C80FNANXX
Run name:	151026_D00408_0310_C80FNANXX
Cycles:	125
End type:	Paired End
Yield (Gbases):	47.60
Total sequences:	190,412,206

Sequences were sampled, trimmed to 36 bases and mapped to 30 reference genomes (see list below) using Bowtie.

The reference genomes are sorted in the tables below according to how many sequences have been mapped. Sequence reads often align to multiple genomes. Each sequence is assigned to the genome with the most aligned sequences. The 'assigned' column contains the number of sequences that align to that particular genome but not also to another genome listed higher in the table, i.e. with more overall matches.

Sequences containing adapters were found by ungapped alignment using Exonerate.

Datasets: 8 |

8

Yield (Gbases):	47.60
Sequences:	190,412,206
Sampled:	100,000

Reference ID	Species/Reference Genome	Aligned	Aligned %	Error rate	Assigned	Assigned %
mmu.mm10	Mus musculus (mouse)	86513	86.5%	0.56%	86513	86.5%
phix.Illumina.RTA	Phi X 174	7550	7.6%	0.12%	7550	7.6%
Other	28 others				770	0.8%
Unmapped					5167	5.2%
Adapter		352	0.4%

Sample details

Sample ID	Sample name	Group	Owner	Sequence type	End type	Experiment type	Species	Control
SLX-10776	NF14 ES	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	NF17 YC	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	NF17ES	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	NfI/+	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	NfI/-	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	NF14 YC	SCI Maike Paramor	Maike Paramor	RNA	Paired End	RNASeq	Mus musculus (mouse)	No
SLX-10776	Control		phix	RNA	Paired End	RNASeq	Phi X 174	Yes

Reference Genomes

Sequences were aligned to the following reference genomes (30 in total)

Anolis carolinensis (anole lizard)
Arabidopsis thaliana (thale cress)
Bacteria
Caenorhabditis elegans (roundworm)
Callithrix jacchus (marmoset)
Canis familiaris (dog)
Cavia porcellus (guinea pig)
Danio rerio (zebrafish)
Dictyostelium discoideum (slime mold)
Drosophila melanogaster (fruitfly)
Escherichia coli
Fungi
Gallus gallus (chicken)
Gorilla gorilla
Homo sapiens (human)
Macaca mulatta (Rhesus macaque)
Monodelphis domestica (opossum)
Mus musculus (mouse)
Nomascus leucogenys (northern white-cheeked gibbon)
Oryctolagus cuniculus (rabbit)
Pan troglodytes (chimpanzee)
Papio anubis (olive baboon)
Phi X 174
Pongo abelii (orangutan)
Rattus norvegicus (rat)
Ribomsomal RNA (human)
Saccharomyces cerevisiae (brewer's yeast)
Tetraodon nigroviridis (pufferfish)
Viruses
Xenopus laevis (African clawed frog)