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# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
CHK 2640041e c45785f6 5d1e6d03
# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
SN raw total sequences: 13 # excluding supplementary and secondary reads
SN filtered sequences: 0
SN sequences: 13
SN is sorted: 1 # sorted by coordinate
SN 1st fragments: 7
SN last fragments: 6
SN reads mapped: 13
SN reads mapped and paired: 13 # paired-end technology bit set + both mates mapped
SN reads unmapped: 0
SN reads properly paired: 12 # proper-pair bit set
SN reads paired: 13 # paired-end technology bit set
SN reads duplicated: 0 # PCR or optical duplicate bit set
SN reads MQ0: 0 # mapped and MQ=0
SN reads QC failed: 0
SN non-primary alignments: 0
SN supplementary alignments: 0
SN total length: 130 # ignores clipping
SN total first fragment length: 70 # ignores clipping
SN total last fragment length: 60 # ignores clipping
SN bases mapped: 130 # ignores clipping
SN bases mapped (cigar): 130 # 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: 13.5
SN insert size average: 34.0
SN insert size standard deviation: 0.0
SN inward oriented pairs: 6
SN outward oriented pairs: 0
SN pairs with other orientation: 0
SN pairs on different chromosomes: 0
SN percentage of properly paired reads (%): 92.3
# 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 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 2 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 3 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 4 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 5 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 6 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 7 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 8 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 9 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
FFQ 10 0 1 0 1 0 1 0 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 0 1 0 1 0 1 0 1 0 1 0 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 2
GCF 64.82 1
GCF 74.87 2
GCF 84.92 1
# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
GCL 19.85 0
GCL 44.72 2
GCL 54.77 1
GCL 64.82 2
GCL 74.87 1
# 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 30.77 15.38 15.38 38.46 0.00 0.00
GCC 2 30.77 23.08 30.77 15.38 0.00 0.00
GCC 3 15.38 61.54 15.38 7.69 0.00 0.00
GCC 4 15.38 15.38 53.85 15.38 0.00 0.00
GCC 5 23.08 15.38 30.77 30.77 0.00 0.00
GCC 6 30.77 30.77 15.38 23.08 0.00 0.00
GCC 7 0.00 53.85 23.08 23.08 0.00 0.00
GCC 8 15.38 15.38 53.85 15.38 0.00 0.00
GCC 9 38.46 7.69 30.77 23.08 0.00 0.00
GCC 10 30.77 30.77 30.77 7.69 0.00 0.00
# ACGT content per cycle, read oriented. Use `grep ^GCT | 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 [%]
GCT 1 53.85 23.08 7.69 15.38
GCT 2 15.38 23.08 30.77 30.77
GCT 3 7.69 23.08 53.85 15.38
GCT 4 7.69 53.85 15.38 23.08
GCT 5 38.46 30.77 15.38 15.38
GCT 6 15.38 15.38 30.77 38.46
GCT 7 7.69 15.38 61.54 15.38
GCT 8 7.69 53.85 15.38 23.08
GCT 9 38.46 23.08 15.38 23.08
GCT 10 7.69 23.08 38.46 30.77
# 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 42.86 28.57 14.29 14.29 0.00 0.00
FBC 2 14.29 28.57 42.86 14.29 0.00 0.00
FBC 3 14.29 42.86 28.57 14.29 0.00 0.00
FBC 4 14.29 28.57 28.57 28.57 0.00 0.00
FBC 5 28.57 28.57 28.57 14.29 0.00 0.00
FBC 6 14.29 28.57 28.57 28.57 0.00 0.00
FBC 7 0.00 28.57 42.86 28.57 0.00 0.00
FBC 8 14.29 28.57 28.57 28.57 0.00 0.00
FBC 9 42.86 14.29 28.57 14.29 0.00 0.00
FBC 10 14.29 28.57 42.86 14.29 0.00 0.00
# ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
FTC 14 20 22 14 0
# 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 0.00 16.67 66.67 0.00 0.00
LBC 2 50.00 16.67 16.67 16.67 0.00 0.00
LBC 3 16.67 83.33 0.00 0.00 0.00 0.00
LBC 4 16.67 0.00 83.33 0.00 0.00 0.00
LBC 5 16.67 0.00 33.33 50.00 0.00 0.00
LBC 6 50.00 33.33 0.00 16.67 0.00 0.00
LBC 7 0.00 83.33 0.00 16.67 0.00 0.00
LBC 8 16.67 0.00 83.33 0.00 0.00 0.00
LBC 9 33.33 0.00 33.33 33.33 0.00 0.00
LBC 10 50.00 33.33 16.67 0.00 0.00 0.00
# ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters
LTC 16 15 17 12 0
# 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 6 6 0 0
# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
RL 10 13
# Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
FRL 10 7
# Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
LRL 10 6
# Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
MAPQ 1 1
MAPQ 3 1
MAPQ 5 1
MAPQ 7 1
MAPQ 9 1
MAPQ 11 1
MAPQ 13 1
MAPQ 15 1
MAPQ 17 1
MAPQ 19 1
MAPQ 21 1
MAPQ 23 1
MAPQ 50 1
# 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 5
COV [2-2] 2 24
COV [3-3] 3 23
COV [4-4] 4 2
# 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
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