Mercurial > repos > devteam > samtools_stats

# CHK, Checksum	[2]Read Names	[3]Sequences	[4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK	cb2d2d82	bcd83869	62ec814e
# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN	raw total sequences:	26
SN	filtered sequences:	0
SN	sequences:	26
SN	is sorted:	1
SN	1st fragments:	14
SN	last fragments:	12
SN	reads mapped:	26
SN	reads mapped and paired:	26	# paired-end technology bit set + both mates mapped
SN	reads unmapped:	0
SN	reads properly paired:	24	# proper-pair bit set
SN	reads paired:	26	# paired-end technology bit set
SN	reads duplicated:	0	# PCR or optical duplicate bit set
SN	reads MQ0:	1	# mapped and MQ=0
SN	reads QC failed:	0
SN	non-primary alignments:	0
SN	total length:	260	# ignores clipping
SN	total first fragment length:	140	# ignores clipping
SN	total last fragment length:	120	# ignores clipping
SN	bases mapped:	260	# ignores clipping
SN	bases mapped (cigar):	206	# more accurate
SN	bases trimmed:	0
SN	bases duplicated:	0
SN	mismatches:	0	# from NM fields
SN	error rate:	0.000000e+00	# mismatches / bases mapped (cigar)
SN	average length:	10
SN	average first fragment length:	10
SN	average last fragment length:	10
SN	maximum length:	10
SN	maximum first fragment length:	10
SN	maximum last fragment length:	10
SN	average quality:	13.1
SN	insert size average:	34.0
SN	insert size standard deviation:	0.0
SN	inward oriented pairs:	12
SN	outward oriented pairs:	0
SN	pairs with other orientation:	0
SN	pairs on different chromosomes:	1
SN	percentage of properly paired reads (%):	92.3
SN	bases inside the target:	42
SN	percentage of target genome with coverage > 0 (%):	100.00
# First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
FFQ	1	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	2	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	3	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	4	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	5	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	6	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	7	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	8	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	9	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
FFQ	10	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0
# Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.
# Columns correspond to qualities and rows to cycles. First column is the cycle number.
LFQ	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	2	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	3	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	4	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	5	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	6	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	7	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	8	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	9	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
LFQ	10	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	1	1	1	1	1	1	1	1	1	0	0	0	0	0	0	0	0	0	0
# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.
GCF	19.85	0
GCF	44.72	1
GCF	54.77	4
GCF	64.82	2
GCF	74.87	4
GCF	84.92	3
# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
GCL	19.85	0
GCL	44.72	2
GCL	59.80	3
GCL	74.87	4
# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
GCC	1	19.23	42.31	15.38	23.08	0.00	0.00
GCC	2	19.23	19.23	46.15	15.38	0.00	0.00
GCC	3	23.08	38.46	19.23	19.23	0.00	0.00
GCC	4	23.08	23.08	38.46	15.38	0.00	0.00
GCC	5	11.54	38.46	26.92	23.08	0.00	0.00
GCC	6	23.08	23.08	34.62	19.23	0.00	0.00
GCC	7	15.38	34.62	26.92	23.08	0.00	0.00
GCC	8	26.92	23.08	38.46	11.54	0.00	0.00
GCC	9	23.08	26.92	26.92	23.08	0.00	0.00
GCC	10	23.08	23.08	38.46	15.38	0.00	0.00
# ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
FBC	1	21.43	42.86	21.43	14.29	0.00	0.00
FBC	2	7.14	28.57	42.86	21.43	0.00	0.00
FBC	3	28.57	35.71	21.43	14.29	0.00	0.00
FBC	4	14.29	28.57	35.71	21.43	0.00	0.00
FBC	5	14.29	35.71	35.71	14.29	0.00	0.00
FBC	6	14.29	28.57	28.57	28.57	0.00	0.00
FBC	7	14.29	28.57	35.71	21.43	0.00	0.00
FBC	8	21.43	28.57	28.57	21.43	0.00	0.00
FBC	9	21.43	21.43	35.71	21.43	0.00	0.00
FBC	10	14.29	28.57	35.71	21.43	0.00	0.00
# ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%]
LBC	1	16.67	41.67	8.33	33.33	0.00	0.00
LBC	2	33.33	8.33	50.00	8.33	0.00	0.00
LBC	3	16.67	41.67	16.67	25.00	0.00	0.00
LBC	4	33.33	16.67	41.67	8.33	0.00	0.00
LBC	5	8.33	41.67	16.67	33.33	0.00	0.00
LBC	6	33.33	16.67	41.67	8.33	0.00	0.00
LBC	7	16.67	41.67	16.67	25.00	0.00	0.00
LBC	8	33.33	16.67	50.00	0.00	0.00	0.00
LBC	9	25.00	33.33	16.67	25.00	0.00	0.00
LBC	10	33.33	16.67	41.67	8.33	0.00	0.00
# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs
IS	0	0	0	0	0
IS	1	0	0	0	0
IS	2	0	0	0	0
IS	3	0	0	0	0
IS	4	0	0	0	0
IS	5	0	0	0	0
IS	6	0	0	0	0
IS	7	0	0	0	0
IS	8	0	0	0	0
IS	9	0	0	0	0
IS	10	0	0	0	0
IS	11	0	0	0	0
IS	12	0	0	0	0
IS	13	0	0	0	0
IS	14	0	0	0	0
IS	15	0	0	0	0
IS	16	0	0	0	0
IS	17	0	0	0	0
IS	18	0	0	0	0
IS	19	0	0	0	0
IS	20	0	0	0	0
IS	21	0	0	0	0
IS	22	0	0	0	0
IS	23	0	0	0	0
IS	24	0	0	0	0
IS	25	0	0	0	0
IS	26	0	0	0	0
IS	27	0	0	0	0
IS	28	0	0	0	0
IS	29	0	0	0	0
IS	30	0	0	0	0
IS	31	0	0	0	0
IS	32	0	0	0	0
IS	33	0	0	0	0
IS	34	12	12	0	0
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL	10	26
# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
FRL	10	14
# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
LRL	10	12
# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)
# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
COV	[1-1]	1	1
COV	[2-2]	2	1
COV	[3-3]	3	2
COV	[4-4]	4	2
COV	[5-5]	5	23
COV	[6-6]	6	13
# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile
GCD	0.0	100.000	0.000	0.000	0.000	0.000	0.000
author	iuc
date	Mon, 29 Jul 2019 08:49:54 -0400
parents	95a7ddf617e7
children	e28839a4b932