Flowcell  AC565BACXX
Run Start  2014-09-04
Read Length  50 single end
HiSeq Sequencing Kit Trueseq v3

Sequencer Software	HiSeq Control Software	2.0
Gerald version     1.8

Alignment Report:

Legend:
Total - total reads considered ( random 10% of total reads sequenced )
Total Unique - total reads aligning to only a single location in the reference
U0 - # of unique hits with 0 mismatches
U1 - # of unique hits with 1 mismatches
U2 - # of unique hits with 2 mismatches
R012 - # of hits aligning to multiple location in the reference with 0,1 or 2 mismatches
NM - # of reads without a match to the reference

Mapping Algorithm : GEM allowing up to 2 mismatches

Lane 7

Sample: B4
Index: GTCCGC
Lab ID: 7924
Application: ChIP Seq
Reference: M.musculus (mm10)

Total	2558021
Total Unique	2032240	79.4%

U0	1846843	72.2%
U1	151651	5.9%
U2	33746	1.3%
R012	333633	13.0%
NM	158492	6.2%

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Lane 7

Sample: 18 4
Index: GTGAAA
Lab ID: 7925
Application: ChIP Seq
Reference: M.musculus (mm10)

Total	2355883
Total Unique	1879333	79.8%

U0	1719559	73.0%
U1	131106	5.6%
U2	28668	1.2%
R012	281457	11.9%
NM	164467	7.0%

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Lane 7

Sample: D1 4
Index: GTGGCC
Lab ID: 7926
Application: ChIP Seq
Reference: M.musculus (mm10)

Total	2732300
Total Unique	2234374	81.8%

U0	2049426	75.0%
U1	153081	5.6%
U2	31867	1.2%
R012	288577	10.6%
NM	176375	6.5%

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Lane 7

Sample: D2 4
Index: GTTTCG
Lab ID: 7927
Application: ChIP Seq
Reference: M.musculus (mm10)

Total	2478527
Total Unique	1998963	80.7%

U0	1839037	74.2%
U1	132309	5.3%
U2	27617	1.1%
R012	278410	11.2%
NM	173913	7.0%

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Lane 7

Sample: D1 27
Index: ACTGAT
Lab ID: 7930
Application: ChIP Seq
Reference: M.musculus (mm10)

Total	2428212
Total Unique	1742879	71.8%

U0	1590379	65.5%
U1	123407	5.1%
U2	29093	1.2%
R012	480603	19.8%
NM	169431	7.0%

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