CRSPR Cas9 treated mice

Gene disruptions in CRSPR/Cas9 treated mice detected by the bidirectional method

Short-reads of a mouse androgen receptor gene targeted by the improved CRISPR/Cas9 system were analyzed by the bidirectional method, and deletions longer than 50 bp were detected in the target gene as well as the other regions of the mouse genome. The target is chromosome X around 98,150,120. Very large insertions and deletions may be false-positive, because of appearance of coincidental same sequence by mutation.

Sequence: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=ERP004393

Reference: Iyer, V. et al. Off-target mutations are rare in Cas9-modified mice. Nat. Methods 12, 479 (2015).

Accession	Junction by 5' to 3' alignment		Junction by 3' to 5' alignment		Type	Size	GRCm38		Target		Genotype	Sequence between junction
	Chromosome	Position	Chromosome	Position			Ref	Alt	Ref	Alt
ERS374108	1	24,684,094	1	24,684,045	insertion	69	7	1	5	3	H	GGTGGTGGTGGTTACAGACCT
ERS374109	1	25,080,709	1	137,017,753	deletion	-111,937,070	14	1	6	3	H	TCTCTCTCTCTCTCTCTCTCTCTCT
ERS374109	1	83,700,487	1	83,700,562	deletion	-96	12	0	5	5	H	TCCCTCTCCCTCTCCCTCTC
ERS374108	1	98,225,840	1	98,225,964	deletion	-128	27	0	5	10	H	ATG
ERS374105	1	104,832,046	1	104,832,105	deletion	-85	10	0	6	3	H	ACACACACACACACACACACACACA
ERS374105	1	104,962,622	1	104,969,611	deletion	-7,002	18	1	8	4	H	TTTTTTTTTTTT
ERS374108	1	175,039,953	1	175,040,039	deletion	-90	16	0	9	4	H	GCA
ERS374108	2	98,058,716	2	98,058,743	deletion	-50	9	1	6	3	H	TATATATATATATATATATATA
ERS374107	2	111,256,375	2	111,256,462	deletion	-96	11	1	9	5	H	ATATATAT
ERS374108	2	131,739,564	2	131,739,626	deletion	-78	18	0	5	3	H	CCTTCCCCTTCCCCT
ERS374107	2	159,060,832	2	159,060,883	deletion	-54	21	0	8	6	H	CT
ERS374109	2	165,802,170	2	165,801,994	insertion	180	14	1	8	6	H	GTGAC
ERS374108	3	11,724,229	3	11,724,496	deletion	-284	12	0	13	8	H	AAGATATCATCTTAGT
ERS374107	3	52,899,684	3	52,899,758	deletion	-78	40	0	11	13	H	TTC
ERS374105	4	125,572,296	4	125,572,176	insertion	133	15	1	7	5	H	CACAGACACAGAAA
ERS374107	4	129,963,119	4	59,276,532	insertion	70,686,591	16	1	11	5	H	CTCTC
ERS374105	4	136,753,857	4	136,754,000	deletion	-147	36	0	18	8	H	AAG
ERS374106	4	136,753,857	4	136,754,000	deletion	-147	36	0	8	12	H	AAG
ERS374107	4	136,753,857	4	136,754,000	deletion	-147	36	0	11	10	H	AAG
ERS374108	4	136,753,857	4	136,754,000	deletion	-147	36	0	9	9	H	AAG
ERS374106	4	139,343,256	4	139,318,173	insertion	25,079	25	0	7	5	H	CCC
ERS374106	4	143,216,092	4	143,216,205	deletion	-126	26	0	9	4	H	CACACACACACA
ERS374108	5	24,117,778	5	24,118,728	deletion	-963	8	0	5	3	H	TTAAGCAGTCTT
ERS374108	5	27,648,703	5	27,648,512	insertion	144	17	1	5	3	H	AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAG
ERS374106	5	35,149,265	5	35,149,494	deletion	-233	47	0	8	9	H	AGG
ERS374109	5	35,149,265	5	35,149,494	deletion	-233	47	0	10	11	H	AGG
ERS374106	5	45,624,549	5	24,256,268	insertion	21,368,251	34	1	15	8	H	GTTACTTATTCAGATGAATTACCTCCAGT
ERS374106	5	109,122,638	5	109,129,530	deletion	-6,914	24	0	8	5	H	AAAAATATAAATAGGCCAATC
ERS374109	5	109,122,638	5	109,129,530	deletion	-6,914	24	0	17	10	H	AAAAATATAAATAGGCCAATC
ERS374108	6	44,120,718	6	44,120,990	deletion	-284	9	0	5	3	H	ACACACACACA
ERS374104	6	66,348,864	6	66,349,475	deletion	-612	29	0	14	11	H
ERS374107	6	66,348,864	6	66,349,475	deletion	-612	29	0	10	9	H
ERS374108	6	66,348,864	6	66,349,475	deletion	-612	29	0	14	9	H
ERS374105	7	18,911,496	7	11,995,403	insertion	6,916,057	27	1	7	4	H	TTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
ERS374109	7	60,654,797	7	60,286,741	insertion	368,083	10	0	6	3	H	CTTCGACCAAAATTAATCAAAAGATGAT
ERS374105	7	115,060,889	7	115,061,294	deletion	-408	30	1	6	3	H	GG
ERS374107	8	98,772,622	8	98,772,686	deletion	-83	16	0	6	3	H	GAGAGGGAGAGGGAGAGG
ERS374105	9	51,555,610	9	51,557,373	deletion	-1,768	26	0	11	13	H	CAAG
ERS374106	9	51,555,610	9	51,557,373	deletion	-1,768	26	0	14	14	H	CAAG
ERS374107	9	51,555,610	9	51,557,373	deletion	-1,768	26	0	9	16	H	CAAG
ERS374108	9	51,555,610	9	51,557,373	deletion	-1,768	26	0	15	12	H	CAAG
ERS374108	9	104,712,102	9	104,712,172	deletion	-66	20	1	5	3	H	CCCTT
ERS374107	10	34,034,584	10	34,034,622	deletion	-54	8	0	5	6	H	TATATATATATATAT
ERS374108	10	34,034,584	10	34,034,622	deletion	-54	8	0	6	13	H	TATATATATATATAT
ERS374107	10	48,973,866	10	48,986,811	deletion	-12,948	40	0	10	9	H	TC
ERS374108	10	48,973,866	10	48,986,811	deletion	-12,948	40	0	10	7	H	TC
ERS374108	10	109,850,836	10	109,850,874	deletion	-72	24	0	11	7	H	AGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA
ERS374105	11	3,230,103	11	3,234,461	deletion	-4,360	36	0	22	13	H	G
ERS374109	11	3,230,103	11	3,234,461	deletion	-4,360	36	0	21	17	H	G
ERS374109	11	3,234,648	11	3,235,578	deletion	-935	45	0	18	11	H	AGGT
ERS374106	11	4,657,653	11	117,576,649	deletion	-112,919,001	16	1	6	4	H	GTGT
ERS374104	11	22,206,024	11	22,208,812	deletion	-2,793	45	0	13	16	H	AAGA
ERS374106	11	22,206,024	11	22,208,812	deletion	-2,793	45	0	6	10	H	AAGA
ERS374109	12	12,092,514	12	12,098,994	deletion	-6,495	29	1	6	3	H	AAAAGATAAGCCAA
ERS374105	12	24,630,896	12	24,630,892	deletion	-53	27	1	8	4	H	GGGGTCTACCCCTGACCTACGCCCCTTGCCCAGGGCTGAGGTGTGACAGGTGGGGG
ERS374109	12	24,630,896	12	24,630,892	deletion	-53	27	1	8	4	H	GGGGTCTACCCCTGACCTACGCCCCTTGCCCAGGGCTGAGGTGTGACAGGTGGGGG
ERS374109	12	92,239,521	12	92,239,731	deletion	-228	21	0	6	3	H	AGGCAGGCAGGCAGGCA
ERS374106	12	105,436,235	12	105,436,106	insertion	87	12	1	6	3	H	ATCCCACCAGCCCAATGCAGTGTACACAAGAGAGTCCTCCA
ERS374108	12	117,944,321	12	117,944,515	deletion	-212	30	1	11	6	H	AAAGAAAAACATAGAGA
ERS374108	13	20,275,673	13	20,275,751	deletion	-93	7	1	6	3	H	CTCCTCCTCCTCCT
ERS374107	13	53,482,565	13	53,482,673	deletion	-116	17	0	5	4	H	GTGTGTG
ERS374108	13	78,087,537	13	78,087,555	deletion	-50	10	0	6	3	H	TATATATATATATATATATATATATATATAT
ERS374108	13	95,461,095	13	95,461,528	deletion	-411	9	0	5	4	H	AGGGAAGGGAAGGGAAGGGAAGG
ERS374106	13	103,228,152	13	103,228,113	insertion	63	17	0	7	4	H	CACATTACACAGACCTTCATAGATG
ERS374109	13	112,824,301	13	112,824,298	deletion	-52	13	0	6	3	H	ACACACACGCGCGCACACACACACACACACACACACACACACACACACACACAC
ERS374104	13	116,465,380	13	116,468,882	deletion	-3,517	19	1	5	6	H	AAAAACATTAAAAA
ERS374105	14	28,641,250	14	28,642,603	deletion	-1,349	41	0	18	11	H	AAATT
ERS374104	14	31,253,061	14	31,253,453	deletion	-395	40	0	29	15	H	AG
ERS374105	14	31,253,061	14	31,253,453	deletion	-395	40	0	17	10	H	AG
ERS374106	14	31,254,311	14	31,254,559	deletion	-251	38	0	13	8	H	GG
ERS374105	14	47,676,826	14	47,683,380	deletion	-6,557	35	0	23	16	H	AG
ERS374106	14	47,676,826	14	47,683,380	deletion	-6,557	35	0	27	15	H	AG
ERS374104	14	47,683,491	14	47,684,720	deletion	-1,231	33	0	15	16	H	G
ERS374105	14	47,683,491	14	47,684,720	deletion	-1,231	33	0	18	11	H	G
ERS374106	14	47,683,491	14	47,684,720	deletion	-1,231	33	0	23	14	H	G
ERS374109	14	47,683,491	14	47,684,720	deletion	-1,231	33	0	24	19	H	G
ERS374106	14	47,684,856	14	47,686,250	deletion	-1,402	23	0	21	18	H	TCAAGGT
ERS374109	14	47,684,856	14	47,686,250	deletion	-1,402	23	0	14	8	H	TCAAGGT
ERS374109	14	47,686,344	14	47,689,946	deletion	-3,605	20	0	11	6	H	AG
ERS374104	14	59,519,004	14	59,519,038	deletion	-54	7	0	6	6	H	TATATATATATATATATAT
ERS374107	14	81,439,993	14	81,440,071	deletion	-60	27	0	8	4	H	ATATTCATATATGTATATA
ERS374104	14	99,194,575	14	99,194,689	deletion	-118	18	0	12	7	H	AAC
ERS374105	14	99,194,575	14	99,194,689	deletion	-118	18	0	7	9	H	AAC
ERS374107	15	44,678,185	15	44,678,367	deletion	-197	13	1	6	3	H	ATCTTTAGACTTTT
ERS374107	16	3,591,447	16	3,591,831	deletion	-397	16	0	8	4	H	GTGTGTGTGTGT
ERS374109	16	10,793,840	16	10,794,956	deletion	-1,126	24	0	8	4	H	CACAAGGTA
ERS374104	16	35,761,968	16	35,762,047	deletion	-51	8	1	5	3	H	AGAGAGAGAGAGAGAGAGAGAAGGAGCTG
ERS374107	16	45,512,593	16	45,518,970	deletion	-6,392	10	1	5	3	H	TCAAAACACTTCTT
ERS374108	16	47,502,608	16	47,502,713	deletion	-106	16	1	6	3	H
ERS374109	17	5,470,888	17	5,471,035	deletion	-152	35	0	10	10	H	CAGA
ERS374108	18	49,793,476	18	49,793,609	deletion	-165	14	0	6	3	H	AGGGAGAGAGGTAAGGAAGGAGGGAGGGAGG
ERS374105	19	11,966,045	19	11,966,089	deletion	-56	11	0	5	5	H	GGCGGCGGCGG
ERS374108	19	50,486,921	19	50,529,041	deletion	-42,123	43	0	12	16	H	GT
ERS374109	19	50,486,921	19	50,529,041	deletion	-42,123	43	0	9	14	H	GT
ERS374108	X	89,414,716	X	89,414,796	deletion	-108	15	0	5	3	H	TGTGTGTGTGTGTGTGTGTGTGTGTGT
ERS374104	X	98,150,098	X	98,150,168	deletion	-58	35	0	11	7	H	TGGGGCGGCCACC
ERS374105	X	98,150,099	X	98,150,174	deletion	-78	35	0	8	6	H	CC
ERS374109	X	98,150,103	X	98,150,171	deletion	-56	35	0	13	8	H	CTGCCTCCCCGAG
ERS374107	X	98,150,120	X	98,150,177	deletion	-60	34	0	12	9	H	GA
ERS374108	X	98,150,120	X	98,150,177	deletion	-60	34	0	10	8	H	GA
ERS374107	X	123,000,254	X	123,662,411	deletion	-662,172	8	1	5	4	H	TTTTTTTTTTTTTT
ERS374106	X	127,841,379	X	127,841,489	deletion	-95	5	1	5	3	H	AACTTTTGGAAGTTAT
ERS374109	Y	90,740,215	Y	90,740,339	deletion	-107	91	0	59	61	H	CTGCTCTGAGACACGCCT
ERS374109	Y	90,741,412	Y	90,741,497	deletion	-113	75	0	46	27	H	GGAGAGACCGGGACAGACAGGCAGAGA