## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics --MAX_INSERT_SIZE 100000   --IS_BISULFITE_SEQUENCED true --INPUT /data_local/16/3A_WT_WGBS_chr2_17k_R1.bam --OUTPUT 3A_WT_WGBS_chr2_17k_R1_alignment_metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY STRICT --REFERENCE_SEQUENCE /data_local/1/hg19_chr2 17k.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --COLLECT_ALIGNMENT_INFORMATION true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Feb 10 18:14:34 UTC 2022

## METRICS CLASS	picard.analysis.AlignmentSummaryMetrics
CATEGORY	TOTAL_READS	PF_READS	PCT_PF_READS	PF_NOISE_READS	PF_READS_ALIGNED	PCT_PF_READS_ALIGNED	PF_ALIGNED_BASES	PF_HQ_ALIGNED_READS	PF_HQ_ALIGNED_BASES	PF_HQ_ALIGNED_Q20_BASES	PF_HQ_MEDIAN_MISMATCHES	PF_MISMATCH_RATE	PF_HQ_ERROR_RATE	PF_INDEL_RATE	MEAN_READ_LENGTH	READS_ALIGNED_IN_PAIRS	PCT_READS_ALIGNED_IN_PAIRS	PF_READS_IMPROPER_PAIRS	PCT_PF_READS_IMPROPER_PAIRS	BAD_CYCLES	STRAND_BALANCE	PCT_CHIMERAS	PCT_ADAPTER	PCT_SOFTCLIP	PCT_HARDCLIP	AVG_POS_3PRIME_SOFTCLIP_LENGTH	SAMPLE	LIBRARY	READ_GROUP
FIRST_OF_PAIR	1095	1095	1	0	1095	1	60083	1095	60083	59110	14	0.266531	0.266531	0	54.87032	1095	1	0	0	0	0.516895	1	0	0	0	0			
SECOND_OF_PAIR	1095	1095	1	0	1095	1	60124	1095	60124	57359	14	0.269077	0.269077	0	54.907763	1095	1	0	0	0	0.483105	1	0	0	0	0			
PAIR	2190	2190	1	0	2190	1	120207	2190	120207	116469	14	0.267805	0.267805	0	54.889041	2190	1	0	0	0	0.5	1	0	0	0	0			

## HISTOGRAM	java.lang.Integer
READ_LENGTH	PAIRED_TOTAL_LENGTH_COUNT	PAIRED_ALIGNED_LENGTH_COUNT
38	134	134
39	116	116
40	116	116
41	114	114
42	96	96
43	86	86
44	92	92
45	94	94
46	92	92
47	58	58
48	86	86
49	74	74
50	60	60
51	40	40
52	54	54
53	48	48
54	36	36
55	32	32
56	32	32
57	28	28
58	16	16
59	28	28
60	14	14
61	14	14
62	12	12
63	8	8
64	4	4
65	2	2
66	12	12
67	6	6
68	10	10
69	10	10
70	8	8
71	10	10
72	6	6
73	12	12
74	2	2
75	6	6
76	7	7
77	16	16
78	26	26
79	207	207
80	266	266

