PromoSer Performance and Statistics

PromoSer alignment statistics

		Analyzed	Mapped	Assigned
EPD	Human	1869	66.67%	68.49%
	Mouse	196	35.20%	40.82%
	Rat	119	21.01%	21.85%
RefSeq	Human	20468	96.69%	97.22%
	Mouse	16635	88.62%	90.46%
	Rat	4780	80.33%	81.55%
mRNA	Human	136794	81.02%	86.45%
	Mouse	50252	78.01%	86.30%
	Rat	11244	77.69%	81.22%
EST	Human	5471602	28.87%	74.75%
	Mouse	4056258	30.10%	74.09%
	Rat	517639	31.14%	52.28%
Gene	Human	73201	0.00%	58.69%
	Mouse	20973	0.00%	51.46%
	Rat	3988	0.00%	35.96%
Total		10386018	30.43%	73.49%

Aanlyzed:Total number of downloaded sequences that remained after keyword filtering.
Mapped:Sequences that passed level 1 filtering and were used for clustering (% of total analyzed).
Assigned:Mapped sequences plus those heuristically assigned to clusters (% of total analyzed).
Note that genomic records were not used for clustering and were always assigned later to clusters.

Clustering statistics

	All	TSS 2-4	TSS 0	TSS 1	TSS 2	TSS 3	TSS 4
Human	46171	32514	9.81%	19.77%	38.61%	29.02%	2.79%
Mouse	38926	20470	6.78%	40.63%	19.57%	32.78%	0.24%
Rat	26973	4785	34.99%	47.27%	6.64%	11.01%	0.10%

The TSS columns represent the number or fraction from the total number of clusters where the highest quality TSS in the cluster is at the quality level shown. This is a graph of the above table data. The x-axis represents the number of clusters.

Genomic extensions for RefSeq data

	Human	Mouse	Rat
<100	28.82%	37.95%	36.92%
<500	27.00%	27.14%	23.13%
<2000	12.11%	9.10%	11.72%
<5000	5.06%	6.09%	7.29%
<10000	4.63%	4.56%	6.13%
<20000	5.37%	4.40%	4.55%
<50000	7.14%	4.97%	5.59%
<100000	4.67%	2.79%	2.31%
<500000	4.56%	2.38%	2.13%
>500000	0.63%	0.63%	0.24%
>20	62.17%	62.79%	41.59%

The last row of the table shows the fraction of RefSeq sequences that had a genomic extension larger than 20bp, out of all assigned RefSeq records (see top table). The distribution of those extensions (from 20bp and above, as a fraction of all extensions over 20bp) are shown in the figure.