## htsjdk.samtools.metrics.StringHeader
# CollectMultipleMetrics INPUT=in/sample.bam OUTPUT=picard/cmm METRIC_ACCUMULATION_LEVEL=[ALL_READS, LIBRARY, SAMPLE, READ_GROUP] PROGRAM=[CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectInsertSizeMetrics, CollectQualityYieldMetrics, CollectSequencingArtifactMetrics, MeanQualityByCycle, QualityScoreDistribution] REFERENCE_SEQUENCE=in/reference.shifted.for.crams.fasta    ASSUME_SORTED=true STOP_AFTER=0 INCLUDE_UNPAIRED=false DO_NOT_CREATE_PLOTS=false 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 21:42:13 HST 2026

## METRICS CLASS	picard.analysis.InsertSizeMetrics
MEDIAN_INSERT_SIZE	MODE_INSERT_SIZE	MEDIAN_ABSOLUTE_DEVIATION	MIN_INSERT_SIZE	MAX_INSERT_SIZE	MEAN_INSERT_SIZE	STANDARD_DEVIATION	READ_PAIRS	PAIR_ORIENTATION	WIDTH_OF_10_PERCENT	WIDTH_OF_20_PERCENT	WIDTH_OF_30_PERCENT	WIDTH_OF_40_PERCENT	WIDTH_OF_50_PERCENT	WIDTH_OF_60_PERCENT	WIDTH_OF_70_PERCENT	WIDTH_OF_80_PERCENT	WIDTH_OF_90_PERCENT	WIDTH_OF_95_PERCENT	WIDTH_OF_99_PERCENT	SAMPLE	LIBRARY	READ_GROUP
335.5	321	65.5	112	899	357.864017	120.944	478	FR	31	57	79	105	131	169	213	281	395	533	865			
335.5	321	65.5	112	899	357.864017	120.944	478	FR	31	57	79	105	131	169	213	281	395	533	865	NA12891		
321	253	68	112	899	346.933824	129.220667	272	FR	31	57	83	103	137	165	213	281	381	565	945	NA12891	Pond-492101	
354	229	63.5	136	731	372.296117	107.674735	206	FR	33	61	75	105	127	159	187	251	381	465	583	NA12891	NormPond-544932	
321	253	68	112	899	346.933824	129.220667	272	FR	31	57	83	103	137	165	213	281	381	565	945	NA12891	Pond-492101	NA12891.r1
354	229	63.5	136	731	372.296117	107.674735	206	FR	33	61	75	105	127	159	187	251	381	465	583	NA12891	NormPond-544932	NA12891.r2

## HISTOGRAM	java.lang.Integer
insert_size	All_Reads.fr_count	NA12891.fr_count	Pond-492101.fr_count	NormPond-544932.fr_count	NA12891.r1.fr_count	NA12891.r2.fr_count
112	1	1	1	0	1	0
128	1	1	1	0	1	0
134	1	1	1	0	1	0
136	1	1	0	1	0	1
156	1	1	1	0	1	0
158	1	1	0	1	0	1
168	1	1	1	0	1	0
169	1	1	1	0	1	0
171	1	1	1	0	1	0
172	1	1	1	0	1	0
176	1	1	0	1	0	1
177	1	1	1	0	1	0
179	2	2	1	1	1	1
180	1	1	1	0	1	0
181	2	2	2	0	2	0
185	1	1	1	0	1	0
187	1	1	1	0	1	0
188	3	3	3	0	3	0
192	1	1	1	0	1	0
194	3	3	3	0	3	0
195	1	1	1	0	1	0
199	1	1	1	0	1	0
205	1	1	1	0	1	0
206	1	1	1	0	1	0
207	2	2	2	0	2	0
212	1	1	0	1	0	1
216	1	1	1	0	1	0
217	1	1	1	0	1	0
219	1	1	1	0	1	0
221	3	3	3	0	3	0
224	1	1	1	0	1	0
225	1	1	0	1	0	1
226	1	1	1	0	1	0
227	1	1	0	1	0	1
228	3	3	1	2	1	2
229	4	4	1	3	1	3
231	1	1	1	0	1	0
232	2	2	2	0	2	0
234	1	1	1	0	1	0
235	2	2	1	1	1	1
236	2	2	1	1	1	1
238	1	1	0	1	0	1
239	1	1	1	0	1	0
241	2	2	1	1	1	1
243	4	4	3	1	3	1
244	1	1	1	0	1	0
245	1	1	1	0	1	0
246	3	3	2	1	2	1
247	1	1	1	0	1	0
248	1	1	1	0	1	0
249	2	2	1	1	1	1
251	2	2	2	0	2	0
252	1	1	1	0	1	0
253	4	4	4	0	4	0
254	2	2	1	1	1	1
255	1	1	1	0	1	0
258	2	2	2	0	2	0
259	1	1	1	0	1	0
260	1	1	1	0	1	0
261	1	1	0	1	0	1
262	2	2	2	0	2	0
264	1	1	1	0	1	0
265	2	2	0	2	0	2
266	3	3	2	1	2	1
267	1	1	0	1	0	1
268	2	2	1	1	1	1
269	3	3	0	3	0	3
270	1	1	1	0	1	0
271	1	1	1	0	1	0
272	2	2	2	0	2	0
273	2	2	0	2	0	2
274	2	2	1	1	1	1
275	2	2	1	1	1	1
276	3	3	2	1	2	1
277	2	2	0	2	0	2
278	2	2	2	0	2	0
279	4	4	4	0	4	0
280	2	2	2	0	2	0
281	1	1	0	1	0	1
282	1	1	1	0	1	0
284	2	2	2	0	2	0
285	4	4	1	3	1	3
288	3	3	2	1	2	1
289	4	4	1	3	1	3
290	3	3	2	1	2	1
291	4	4	2	2	2	2
292	1	1	1	0	1	0
293	1	1	0	1	0	1
294	3	3	1	2	1	2
295	4	4	3	1	3	1
296	2	2	1	1	1	1
297	4	4	2	2	2	2
298	2	2	1	1	1	1
299	2	2	2	0	2	0
300	2	2	1	1	1	1
301	2	2	0	2	0	2
302	1	1	1	0	1	0
304	2	2	0	2	0	2
305	4	4	4	0	4	0
306	5	5	2	3	2	3
307	1	1	0	1	0	1
309	2	2	1	1	1	1
310	1	1	0	1	0	1
311	2	2	1	1	1	1
313	5	5	4	1	4	1
314	2	2	1	1	1	1
315	1	1	1	0	1	0
316	2	2	1	1	1	1
317	1	1	0	1	0	1
318	2	2	0	2	0	2
319	3	3	2	1	2	1
320	6	6	3	3	3	3
321	7	7	4	3	4	3
322	3	3	1	2	1	2
323	1	1	1	0	1	0
324	3	3	1	2	1	2
325	2	2	0	2	0	2
327	1	1	1	0	1	0
328	1	1	0	1	0	1
329	2	2	0	2	0	2
330	1	1	0	1	0	1
331	2	2	1	1	1	1
332	1	1	1	0	1	0
333	1	1	1	0	1	0
335	2	2	2	0	2	0
336	2	2	1	1	1	1
338	2	2	2	0	2	0
339	2	2	1	1	1	1
340	1	1	0	1	0	1
343	3	3	0	3	0	3
344	2	2	2	0	2	0
346	4	4	3	1	3	1
347	1	1	0	1	0	1
349	3	3	2	1	2	1
350	2	2	1	1	1	1
352	1	1	1	0	1	0
353	1	1	0	1	0	1
354	2	2	0	2	0	2
355	2	2	2	0	2	0
357	3	3	2	1	2	1
359	3	3	2	1	2	1
360	4	4	2	2	2	2
361	1	1	1	0	1	0
362	1	1	1	0	1	0
363	3	3	2	1	2	1
364	3	3	1	2	1	2
365	2	2	2	0	2	0
366	1	1	1	0	1	0
367	1	1	0	1	0	1
368	1	1	1	0	1	0
369	3	3	3	0	3	0
370	4	4	2	2	2	2
372	3	3	1	2	1	2
373	2	2	1	1	1	1
374	1	1	0	1	0	1
375	5	5	3	2	3	2
380	3	3	1	2	1	2
381	1	1	0	1	0	1
382	3	3	1	2	1	2
384	2	2	2	0	2	0
385	1	1	1	0	1	0
386	1	1	0	1	0	1
387	3	3	2	1	2	1
388	3	3	1	2	1	2
389	4	4	3	1	3	1
391	4	4	2	2	2	2
392	1	1	1	0	1	0
393	2	2	1	1	1	1
394	2	2	1	1	1	1
395	1	1	0	1	0	1
397	1	1	1	0	1	0
398	1	1	1	0	1	0
400	2	2	1	1	1	1
401	1	1	1	0	1	0
402	1	1	0	1	0	1
403	2	2	0	2	0	2
404	2	2	1	1	1	1
406	1	1	0	1	0	1
407	4	4	3	1	3	1
408	1	1	0	1	0	1
410	2	2	0	2	0	2
411	1	1	1	0	1	0
413	2	2	0	2	0	2
417	1	1	0	1	0	1
418	2	2	0	2	0	2
419	1	1	1	0	1	0
420	1	1	0	1	0	1
421	2	2	2	0	2	0
422	1	1	0	1	0	1
425	2	2	1	1	1	1
426	2	2	1	1	1	1
427	1	1	1	0	1	0
429	1	1	0	1	0	1
432	2	2	1	1	1	1
436	3	3	0	3	0	3
439	2	2	2	0	2	0
440	1	1	0	1	0	1
441	1	1	1	0	1	0
442	1	1	0	1	0	1
443	2	2	1	1	1	1
446	4	4	2	2	2	2
447	2	2	1	1	1	1
448	3	3	1	2	1	2
452	2	2	1	1	1	1
454	1	1	1	0	1	0
455	1	1	0	1	0	1
460	2	2	0	2	0	2
461	1	1	1	0	1	0
463	2	2	1	1	1	1
468	1	1	1	0	1	0
470	2	2	2	0	2	0
474	1	1	1	0	1	0
475	3	3	1	2	1	2
478	1	1	0	1	0	1
479	1	1	0	1	0	1
486	1	1	1	0	1	0
487	3	3	1	2	1	2
488	1	1	0	1	0	1
493	1	1	1	0	1	0
497	1	1	0	1	0	1
500	1	1	1	0	1	0
502	1	1	1	0	1	0
504	1	1	1	0	1	0
505	3	3	3	0	3	0
507	1	1	0	1	0	1
511	1	1	1	0	1	0
512	1	1	0	1	0	1
514	1	1	1	0	1	0
515	1	1	1	0	1	0
519	1	1	0	1	0	1
524	1	1	1	0	1	0
528	1	1	0	1	0	1
532	1	1	1	0	1	0
537	1	1	0	1	0	1
538	1	1	0	1	0	1
540	1	1	1	0	1	0
543	1	1	0	1	0	1
544	1	1	0	1	0	1
546	1	1	0	1	0	1
549	1	1	0	1	0	1
550	2	2	1	1	1	1
556	2	2	2	0	2	0
559	1	1	0	1	0	1
564	1	1	0	1	0	1
565	1	1	1	0	1	0
572	1	1	0	1	0	1
581	1	1	0	1	0	1
586	1	1	0	1	0	1
587	1	1	1	0	1	0
589	1	1	1	0	1	0
601	2	2	0	2	0	2
603	1	1	1	0	1	0
612	1	1	1	0	1	0
614	1	1	0	1	0	1
620	2	2	0	2	0	2
621	1	1	1	0	1	0
632	2	2	1	1	1	1
638	1	1	0	1	0	1
645	1	1	0	1	0	1
655	1	1	1	0	1	0
662	1	1	1	0	1	0
679	1	1	1	0	1	0
725	2	2	2	0	2	0
726	1	1	0	1	0	1
731	1	1	0	1	0	1
767	1	1	1	0	1	0
788	1	1	1	0	1	0
793	1	1	1	0	1	0
879	1	1	1	0	1	0
899	1	1	1	0	1	0

