## htsjdk.samtools.metrics.StringHeader
# CollectOxoGMetrics INPUT=in/sample.bam OUTPUT=picard/oxog.oxog_metrics REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 INCLUDE_NON_PF_READS=true USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:43:06 HST 2026

## METRICS CLASS	picard.analysis.CollectOxoGMetrics$CpcgMetrics
SAMPLE_ALIAS	LIBRARY	CONTEXT	TOTAL_SITES	TOTAL_BASES	REF_NONOXO_BASES	REF_OXO_BASES	REF_TOTAL_BASES	ALT_NONOXO_BASES	ALT_OXO_BASES	OXIDATION_ERROR_RATE	OXIDATION_Q	C_REF_REF_BASES	G_REF_REF_BASES	C_REF_ALT_BASES	G_REF_ALT_BASES	C_REF_OXO_ERROR_RATE	C_REF_OXO_Q	G_REF_OXO_ERROR_RATE	G_REF_OXO_Q
NA12891	Pond-492101	CCA	111	3090	1432	1649	3081	2	7	0.001618	27.909885	1167	1914	0	9	0	100	0.00468	23.297368
NA12891	NormPond-544932	CCA	113	2576	1296	1271	2567	4	5	0.000388	34.109459	1060	1507	0	9	0	100	0.005937	22.264567
NA12891	Pond-492101	ACC	49	1384	659	725	1384	0	0	0.000723	31.411361	604	780	0	0	0	100	0	100
NA12891	NormPond-544932	ACC	49	1137	557	580	1137	0	0	0.00088	30.557605	542	595	0	0	0	100	0	100
NA12891	Pond-492101	CCC	74	2161	1071	1090	2161	0	0	0.000463	33.346548	953	1208	0	0	0	100	0	100
NA12891	NormPond-544932	CCC	74	1798	913	884	1797	0	1	0.000556	32.547897	852	945	1	0	0.001172	29.30949	0	100
NA12891	Pond-492101	GCA	67	1979	954	1025	1979	0	0	0.000505	32.964458	1092	887	0	0	0	100	0	100
NA12891	NormPond-544932	GCA	65	1656	792	863	1655	0	1	0.000604	32.190603	889	766	1	0	0.001124	29.4939	0	100
NA12891	Pond-492101	TCT	113	3468	1787	1681	3468	0	0	0.000288	35.400791	1084	2384	0	0	0	100	0	100
NA12891	NormPond-544932	TCT	114	2681	1352	1328	2680	0	1	0.000373	34.282968	912	1768	1	0	0.001095	29.604708	0	100
NA12891	Pond-492101	ACG	8	155	81	74	155	0	0	0.006452	21.903317	122	33	0	0	0	100	0	100
NA12891	NormPond-544932	ACG	8	127	69	58	127	0	0	0.007874	21.038037	101	26	0	0	0	100	0	100
NA12891	Pond-492101	CCG	11	441	208	233	441	0	0	0.002268	26.444386	149	292	0	0	0	100	0	100
NA12891	NormPond-544932	CCG	11	355	178	177	355	0	0	0.002817	25.502284	133	222	0	0	0	100	0	100
NA12891	Pond-492101	GCC	54	1564	777	787	1564	0	0	0.000639	31.942367	738	826	0	0	0	100	0	100
NA12891	NormPond-544932	GCC	55	1395	725	670	1395	0	0	0.000717	31.445742	681	714	0	0	0	100	0	100
NA12891	Pond-492101	GCG	10	319	166	153	319	0	0	0.003135	25.037907	183	136	0	0	0	100	0	100
NA12891	NormPond-544932	GCG	12	261	131	130	261	0	0	0.003831	24.166405	141	120	0	0	0	100	0	100
NA12891	Pond-492101	ACT	73	2076	1053	1023	2076	0	0	0.000482	33.172273	757	1319	0	0	0	100	0	100
NA12891	NormPond-544932	ACT	73	1767	914	853	1767	0	0	0.000566	32.472365	641	1126	0	0	0	100	0	100
NA12891	Pond-492101	TCA	88	2591	1217	1374	2591	0	0	0.000386	34.134674	1323	1268	0	0	0	100	0	100
NA12891	NormPond-544932	TCA	87	2188	1148	1039	2187	1	0	0.000457	33.400473	1095	1092	1	0	0.000912	30.398106	0	100
NA12891	Pond-492101	CCT	109	3277	1529	1747	3276	1	0	0.000305	35.154764	1340	1936	0	1	0	100	0.000516	32.871296
NA12891	NormPond-544932	CCT	109	2595	1388	1206	2594	1	0	0.000385	34.141374	1154	1440	0	1	0	100	0.000694	31.58664
NA12891	Pond-492101	TCC	127	3878	1725	2152	3877	0	1	0.000258	35.886078	1338	2539	1	0	0.000747	31.267806	0	100
NA12891	NormPond-544932	TCC	129	3017	1605	1411	3016	1	0	0.000331	34.795753	1146	1870	0	1	0	100	0.000534	32.720738
NA12891	Pond-492101	GCT	55	1471	754	717	1471	0	0	0.00068	31.676127	661	810	0	0	0	100	0	100
NA12891	NormPond-544932	GCT	56	1281	653	628	1281	0	0	0.000781	31.075491	591	690	0	0	0	100	0	100
NA12891	Pond-492101	TCG	3	97	49	48	97	0	0	0.010309	19.867717	23	74	0	0	0	100	0	100
NA12891	NormPond-544932	TCG	5	94	38	56	94	0	0	0.010638	19.731279	26	68	0	0	0	100	0	100
NA12891	Pond-492101	ACA	98	2938	1465	1469	2934	2	2	0.00034	34.680518	1567	1367	2	2	0	100	0.000186	37.299664
NA12891	NormPond-544932	ACA	98	2450	1217	1233	2450	0	0	0.000408	33.891661	1304	1146	0	0	0	100	0	100


