## htsjdk.samtools.metrics.StringHeader
# CollectAlignmentSummaryMetrics --MAX_INSERT_SIZE 100000   --IS_BISULFITE_SEQUENCED true --INPUT /data_local/6/3A_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 17:31:40 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
UNPAIRED	1397	1397	1	0	1397	1	78841	1397	78841	77340	14	0.262287	0.262287	0	56.435934	0	0	0	0	0	0.526843	0	0	0	0	0			

## HISTOGRAM	java.lang.Integer
READ_LENGTH	UNPAIRED_TOTAL_LENGTH_COUNT	UNPAIRED_ALIGNED_LENGTH_COUNT
38	81	81
39	69	69
40	66	66
41	70	70
42	57	57
43	54	54
44	57	57
45	57	57
46	52	52
47	36	36
48	54	54
49	41	41
50	34	34
51	27	27
52	29	29
53	35	35
54	23	23
55	24	24
56	18	18
57	20	20
58	12	12
59	19	19
60	10	10
61	10	10
62	6	6
63	6	6
64	3	3
65	1	1
66	6	6
67	4	4
68	6	6
69	6	6
70	4	4
71	5	5
72	4	4
73	7	7
74	2	2
75	5	5
76	6	6
77	13	13
78	22	22
79	81	81
80	141	141
81	4	4
82	3	3
83	10	10
84	36	36
85	61	61

