Does Google drop links from page rank N/A sources?

[AMA-DataSet]

Hi Everyone,
I've started doing some link analysis on one of my site that has over nearly 800 links in total (which I got from the webmaster tools downloading the latest links).

When I go on to Google and use the "link:www.mysite.com" directive it will only display 12 links. Does this mean Google is only counting 12 links from the link profile?

Iv checked the freshness of some the links it wasn't displaying within Google to check they hadn't all expired. Links from march 2013 still don't appear.

This sites link profile has been untouched for at least a year now and is full of directories many of which have a page rank of N/A hence my question. (I'm surprised it hasn't been hit by penguin!)

Thanks in advance.

[Chris.Menke]

Wow, I hadn't seen the link:mydomain search query in a while.

First of all, I woulnd't bother with that search--it's not anywhere close to accurate and it doens't indicate anything that's very useful to you.  Links to your site from other domain may well be counting for or against you and you should start with the opensiteexplorer.org tool to get a better idea of you back links.  However, that tool my not even show you all of them-especially if they are on really low quality pages on really low quality domains.  You may also check majesticseo.com and ahrefs.com as alternative sources.

If you do have a bunch of unnatural back links, now might be a good time to start working to get them removed.

[AMA-DataSet]

Thanks Chris,
I have noticed a great amount of inconstancies between each of the linking analysis software (wish they all had the same its would make things so much easier haha) is there a particular link analysis software you would recommend?

I use open-site explorer, a free link analysis tool by Internet Marketing Ninjas and web master tools at the minute.

[Chris.Menke]

For most purposes, OSE works very well and provides a great amount of detail about each link--plus, it is included with your membership. It's your best place to start and though it takes some time to feel comfortable with the metrics, the more you use it the better you'll understand it.