Flowcell  AC7Y5YACXX
Run Start  2015-09-25
Read Length  50 single end
HiSeq Sequencing Kit Trueseq v3

Sequencer Software	HiSeq Control Software	2.2.58
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_1.7.1 (build 1.819 (beta)) allowing up to 2 mismatches

Lane 5

Sample: BiPS P3
Index: CGATGT
Lab ID: 11525
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	2305707
Total Unique	1256818	54.5%

U0	1126877	48.9%
U1	107284	4.7%
U2	22657	1.0%
R012	168511	7.3%
NM	799168	34.7%

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Lane 5

Sample: BiPS P20
Index: TGACCA
Lab ID: 11526
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	7079594
Total Unique	2883353	40.7%

U0	2569812	36.3%
U1	257052	3.6%
U2	56489	0.8%
R012	382589	5.4%
NM	3617766	51.1%

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Lane 5

Sample: MAC iPS P3
Index: GCCAAT
Lab ID: 11527
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	5141618
Total Unique	1666129	32.4%

U0	1479465	28.8%
U1	150097	2.9%
U2	36567	0.7%
R012	278771	5.4%
NM	3047100	59.3%

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Lane 5

Sample: MAC iPS P20
Index: CAGATC
Lab ID: 11528
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	2265379
Total Unique	1129463	49.9%

U0	1007802	44.5%
U1	99574	4.4%
U2	22087	1.0%
R012	159700	7.0%
NM	895824	39.5%

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Lane 5

Sample: Mef iPS P3
Index: CTTGTA
Lab ID: 11529
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	2379059
Total Unique	1067769	44.9%

U0	951162	40.0%
U1	95141	4.0%
U2	21466	0.9%
R012	148573	6.2%
NM	1085058	45.6%

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Lane 5

Sample: Mef iPS P20
Index: CCGTCC
Lab ID: 11530
Application: ChIP Seq
Reference: M.musculus (GRCm38.dna)

Total	3686479
Total Unique	1438225	39.0%

U0	1285628	34.9%
U1	126376	3.4%
U2	26221	0.7%
R012	161731	4.4%
NM	2007710	54.5%

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