HTSMultiQC-cleaning-report: MultiQC Report

Processing Overview

General statistics from the HTStream pipeline.

Preprocessing Statistics

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Fragment Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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Basepair Reduction

Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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hts_Stats

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ²²/₂₂ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
mouse_110_WT_C	100.00%	91.17%	83.13%	52.92%	0.0010%	initial stats
mouse_110_WT_NC	100.00%	91.60%	88.51%	51.47%	0.0012%	initial stats
mouse_148_WT_C	100.00%	93.02%	87.44%	51.34%	0.0011%	initial stats
mouse_148_WT_NC	100.00%	90.50%	86.38%	52.19%	0.0010%	initial stats
mouse_158_WT_C	100.00%	92.98%	89.09%	50.91%	0.0008%	initial stats
mouse_158_WT_NC	100.00%	92.43%	86.56%	52.33%	0.0009%	initial stats
mouse_183_KOMIR150_C	100.00%	93.14%	87.45%	51.91%	0.0009%	initial stats
mouse_183_KOMIR150_NC	100.00%	91.48%	82.11%	54.19%	0.0009%	initial stats
mouse_198_KOMIR150_C	100.00%	93.11%	88.20%	51.73%	0.0011%	initial stats
mouse_198_KOMIR150_NC	100.00%	92.75%	88.15%	51.53%	0.0009%	initial stats
mouse_206_KOMIR150_C	100.00%	90.60%	72.35%	56.37%	0.0009%	initial stats
mouse_206_KOMIR150_NC	100.00%	86.34%	77.66%	56.02%	0.0008%	initial stats
mouse_2670_KOTet3_C	100.00%	92.82%	88.06%	51.27%	0.0007%	initial stats
mouse_2670_KOTet3_NC	100.00%	92.57%	88.49%	51.13%	0.0009%	initial stats
mouse_7530_KOTet3_C	100.00%	92.75%	86.49%	51.62%	0.0011%	initial stats
mouse_7530_KOTet3_NC	100.00%	92.06%	86.86%	51.13%	0.0008%	initial stats
mouse_7531_KOTet3_C	100.00%	91.41%	86.24%	51.24%	0.0007%	initial stats
mouse_7532_WT_NC	100.00%	93.26%	87.83%	51.32%	0.0009%	initial stats
mouse_H510_WT_C	100.00%	92.09%	85.76%	52.19%	0.0008%	initial stats
mouse_H510_WT_NC	100.00%	92.06%	88.84%	51.00%	0.0010%	initial stats
mouse_H514_WT_C	100.00%	91.22%	84.00%	52.66%	0.0009%	initial stats
mouse_H514_WT_NC	100.00%	92.70%	86.45%	51.26%	0.0010%	initial stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction1`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q301`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q301`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content1`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content1`	None
\|\|	Notes	Notes	Notes	`St_Notes1`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

Notice: Each sample has a uniform read length distribution.

Showing ²²/₂₂ rows and ²/₂ columns.

Sample Name	R1 Read Lengths	R2 Read Lengths
mouse_110_WT_C	101	101
mouse_110_WT_NC	101	101
mouse_148_WT_C	101	101
mouse_148_WT_NC	101	101
mouse_158_WT_C	101	101
mouse_158_WT_NC	101	101
mouse_183_KOMIR150_C	101	101
mouse_183_KOMIR150_NC	101	101
mouse_198_KOMIR150_C	101	101
mouse_198_KOMIR150_NC	101	101
mouse_206_KOMIR150_C	101	101
mouse_206_KOMIR150_NC	101	101
mouse_2670_KOTet3_C	101	101
mouse_2670_KOTet3_NC	101	101
mouse_7530_KOTet3_C	101	101
mouse_7530_KOTet3_NC	101	101
mouse_7531_KOTet3_C	101	101
mouse_7532_WT_NC	101	101
mouse_H510_WT_C	101	101
mouse_H510_WT_NC	101	101
mouse_H514_WT_C	101	101
mouse_H514_WT_NC	101	101

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		R1 Read Lengths	R1 Read Lengths	Length of R1 reads (uniform for each sample).	`St_Read_Lengths_R1_7859356856756`	None
\|\|		R2 Read Lengths	R2 Read Lengths	Length of R2 reads (uniform for each sample).	`St_Read_Lengths_R2_7859356856756`	None

Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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hts_SeqScreener

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Showing ²²/₂₂ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits	Notes
mouse_110_WT_C	15	0.0003%	screen phix
mouse_110_WT_NC	14	0.0003%	screen phix
mouse_148_WT_C	11	0.0002%	screen phix
mouse_148_WT_NC	12	0.0002%	screen phix
mouse_158_WT_C	10	0.0002%	screen phix
mouse_158_WT_NC	8	0.0002%	screen phix
mouse_183_KOMIR150_C	13	0.0003%	screen phix
mouse_183_KOMIR150_NC	18	0.0004%	screen phix
mouse_198_KOMIR150_C	14	0.0003%	screen phix
mouse_198_KOMIR150_NC	16	0.0003%	screen phix
mouse_206_KOMIR150_C	32	0.0006%	screen phix
mouse_206_KOMIR150_NC	25	0.0005%	screen phix
mouse_2670_KOTet3_C	16	0.0003%	screen phix
mouse_2670_KOTet3_NC	14	0.0003%	screen phix
mouse_7530_KOTet3_C	19	0.0004%	screen phix
mouse_7530_KOTet3_NC	11	0.0002%	screen phix
mouse_7531_KOTet3_C	7	0.0001%	screen phix
mouse_7532_WT_NC	15	0.0003%	screen phix
mouse_H510_WT_C	11	0.0002%	screen phix
mouse_H510_WT_NC	17	0.0003%	screen phix
mouse_H514_WT_C	14	0.0003%	screen phix
mouse_H514_WT_NC	14	0.0003%	screen phix

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Sort	Group	Column	Description	ID	Scale
\|\|	PE hits	PE hits	Number of Paired End Reads with Sequence	`Ss_PE_hits1`	None
\|\|	% PE Lost	% PE Hits	Percentage of Paired End Reads Lost	`Ss_PE_%_hits1`	None
\|\|	Notes	Notes	Notes	`Ss_Notes1`	None

hts_SeqScreener 2

A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

Showing ²²/₂₂ rows and ³/₃ columns.

Sample Name	PE hits	% PE Hits	Notes
mouse_110_WT_C	13276	0.2655%	count the number of rRNA reads
mouse_110_WT_NC	14310	0.2862%	count the number of rRNA reads
mouse_148_WT_C	19155	0.3831%	count the number of rRNA reads
mouse_148_WT_NC	25976	0.5195%	count the number of rRNA reads
mouse_158_WT_C	43063	0.8613%	count the number of rRNA reads
mouse_158_WT_NC	17937	0.3587%	count the number of rRNA reads
mouse_183_KOMIR150_C	19972	0.3994%	count the number of rRNA reads
mouse_183_KOMIR150_NC	22591	0.4518%	count the number of rRNA reads
mouse_198_KOMIR150_C	19176	0.3835%	count the number of rRNA reads
mouse_198_KOMIR150_NC	38397	0.7679%	count the number of rRNA reads
mouse_206_KOMIR150_C	14478	0.2896%	count the number of rRNA reads
mouse_206_KOMIR150_NC	16004	0.3201%	count the number of rRNA reads
mouse_2670_KOTet3_C	11008	0.2202%	count the number of rRNA reads
mouse_2670_KOTet3_NC	14155	0.2831%	count the number of rRNA reads
mouse_7530_KOTet3_C	25675	0.5135%	count the number of rRNA reads
mouse_7530_KOTet3_NC	6544	0.1309%	count the number of rRNA reads
mouse_7531_KOTet3_C	21874	0.4375%	count the number of rRNA reads
mouse_7532_WT_NC	17809	0.3562%	count the number of rRNA reads
mouse_H510_WT_C	13006	0.2601%	count the number of rRNA reads
mouse_H510_WT_NC	18728	0.3746%	count the number of rRNA reads
mouse_H514_WT_C	22760	0.4552%	count the number of rRNA reads
mouse_H514_WT_NC	19104	0.3821%	count the number of rRNA reads

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Sort	Group	Column	Description	ID	Scale
\|\|	PE hits	PE hits	Number of Paired End Reads with Sequence	`Ss_PE_hits2`	None
\|\|	% PE Lost	% PE Hits	Percentage of Paired End Reads Lost	`Ss_PE_%_hits2`	None
\|\|	Notes	Notes	Notes	`Ss_Notes2`	None

hts_SuperDeduper

A reference free duplicate read removal tool.

Showing ²²/₂₂ rows and ³/₃ columns.

Sample Name	% Duplicates	% Ignored	Notes
mouse_110_WT_C	38.21%	0.01%	remove PCR duplicates
mouse_110_WT_NC	25.41%	0.01%	remove PCR duplicates
mouse_148_WT_C	26.60%	0.01%	remove PCR duplicates
mouse_148_WT_NC	30.69%	0.01%	remove PCR duplicates
mouse_158_WT_C	22.08%	0.00%	remove PCR duplicates
mouse_158_WT_NC	28.73%	0.01%	remove PCR duplicates
mouse_183_KOMIR150_C	32.76%	0.00%	remove PCR duplicates
mouse_183_KOMIR150_NC	49.15%	0.01%	remove PCR duplicates
mouse_198_KOMIR150_C	27.00%	0.01%	remove PCR duplicates
mouse_198_KOMIR150_NC	24.74%	0.00%	remove PCR duplicates
mouse_206_KOMIR150_C	61.04%	0.00%	remove PCR duplicates
mouse_206_KOMIR150_NC	71.84%	0.00%	remove PCR duplicates
mouse_2670_KOTet3_C	23.74%	0.00%	remove PCR duplicates
mouse_2670_KOTet3_NC	22.47%	0.01%	remove PCR duplicates
mouse_7530_KOTet3_C	29.47%	0.01%	remove PCR duplicates
mouse_7530_KOTet3_NC	21.02%	0.00%	remove PCR duplicates
mouse_7531_KOTet3_C	25.92%	0.00%	remove PCR duplicates
mouse_7532_WT_NC	24.49%	0.00%	remove PCR duplicates
mouse_H510_WT_C	29.44%	0.00%	remove PCR duplicates
mouse_H510_WT_NC	22.39%	0.01%	remove PCR duplicates
mouse_H514_WT_C	35.29%	0.00%	remove PCR duplicates
mouse_H514_WT_NC	24.99%	0.01%	remove PCR duplicates

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Sort	Group	Column	Description	ID	Scale
\|\|	% Duplicates	% Duplicates	Percentage of Duplicate Reads (SE and PE)	`Sd_%_Duplicates1`	None
\|\|	% Ignored	% Ignored	Percentage of Ignored Reads (SE and PE)	`Sd_%_Ignored1`	None
\|\|	Notes	Notes	Notes	`Sd_Notes1`	None

SuperDeduper: Duplicate Saturation

Plots the number of duplicates against the number of unique reads per sample.

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hts_AdapterTrimmer

Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

Showing ²²/₂₂ rows and ⁴/₄ columns.

Sample Name	% Bp Lost	% Adapters	Avg. Bps Trimmed	Notes
mouse_110_WT_C	1.42%	20.17%	14.22	trim adapters
mouse_110_WT_NC	1.35%	20.19%	13.55	trim adapters
mouse_148_WT_C	1.19%	17.82%	13.50	trim adapters
mouse_148_WT_NC	1.40%	19.99%	14.13	trim adapters
mouse_158_WT_C	1.03%	15.93%	13.07	trim adapters
mouse_158_WT_NC	1.14%	16.49%	13.99	trim adapters
mouse_183_KOMIR150_C	1.17%	17.44%	13.54	trim adapters
mouse_183_KOMIR150_NC	1.32%	17.64%	15.17	trim adapters
mouse_198_KOMIR150_C	1.20%	17.93%	13.52	trim adapters
mouse_198_KOMIR150_NC	1.13%	17.11%	13.36	trim adapters
mouse_206_KOMIR150_C	1.55%	19.10%	16.44	trim adapters
mouse_206_KOMIR150_NC	2.07%	22.52%	18.53	trim adapters
mouse_2670_KOTet3_C	1.24%	18.53%	13.50	trim adapters
mouse_2670_KOTet3_NC	1.13%	16.88%	13.54	trim adapters
mouse_7530_KOTet3_C	1.32%	19.67%	13.54	trim adapters
mouse_7530_KOTet3_NC	1.18%	17.58%	13.60	trim adapters
mouse_7531_KOTet3_C	1.30%	19.29%	13.59	trim adapters
mouse_7532_WT_NC	1.28%	19.12%	13.50	trim adapters
mouse_H510_WT_C	1.30%	18.91%	13.87	trim adapters
mouse_H510_WT_NC	1.09%	16.11%	13.69	trim adapters
mouse_H514_WT_C	1.71%	22.55%	15.35	trim adapters
mouse_H514_WT_NC	1.16%	17.55%	13.35	trim adapters

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`At_%_BP_Lost1`	None
\|\|	% Adapters	% Adapters	Percentage of Reads (SE and PE) with an Adapter	`At_%_Adapters1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of basepairs trimmed from reads	`At_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`At_Notes1`	None

AdapterTrimmer: Trimmed Basepairs Composition

Composition of basepairs trimmed from the ends of paired end and single end reads.

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hts_PolyATTrim

Attempts to trim poly-A and poly-T sequences from the end of reads.

Showing ²²/₂₂ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
mouse_110_WT_C	0.05%	62.03%	37.97%	0.10	remove polyA
mouse_110_WT_NC	0.05%	61.28%	38.72%	0.10	remove polyA
mouse_148_WT_C	0.05%	63.65%	36.35%	0.10	remove polyA
mouse_148_WT_NC	0.05%	62.22%	37.78%	0.10	remove polyA
mouse_158_WT_C	0.05%	63.03%	36.97%	0.10	remove polyA
mouse_158_WT_NC	0.05%	62.31%	37.69%	0.09	remove polyA
mouse_183_KOMIR150_C	0.05%	64.20%	35.80%	0.10	remove polyA
mouse_183_KOMIR150_NC	0.05%	64.08%	35.92%	0.11	remove polyA
mouse_198_KOMIR150_C	0.05%	63.54%	36.46%	0.10	remove polyA
mouse_198_KOMIR150_NC	0.05%	63.49%	36.51%	0.10	remove polyA
mouse_206_KOMIR150_C	0.05%	63.11%	36.89%	0.11	remove polyA
mouse_206_KOMIR150_NC	0.06%	63.35%	36.65%	0.12	remove polyA
mouse_2670_KOTet3_C	0.05%	64.14%	35.86%	0.10	remove polyA
mouse_2670_KOTet3_NC	0.05%	59.34%	40.66%	0.10	remove polyA
mouse_7530_KOTet3_C	0.05%	63.13%	36.87%	0.10	remove polyA
mouse_7530_KOTet3_NC	0.05%	61.99%	38.01%	0.10	remove polyA
mouse_7531_KOTet3_C	0.05%	62.58%	37.42%	0.10	remove polyA
mouse_7532_WT_NC	0.05%	61.59%	38.41%	0.10	remove polyA
mouse_H510_WT_C	0.05%	63.77%	36.23%	0.11	remove polyA
mouse_H510_WT_NC	0.05%	63.61%	36.39%	0.11	remove polyA
mouse_H514_WT_C	0.05%	61.70%	38.30%	0.10	remove polyA
mouse_H514_WT_NC	0.05%	60.98%	39.02%	0.11	remove polyA

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Pt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Pt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Pt_%_R2_BP_Lost1`	None
\|\|	Avg. Bps Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Pt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Pt_Notes1`	None

hts_NTrimmer

Trims reads to the longest subsequence that contains no N's.

Showing ²²/₂₂ rows and ⁵/₅ columns.

Sample Name	Total Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	% Discarded	Notes
mouse_110_WT_C	6911	34.26%	65.74%	0.00%	remove any remaining N characters
mouse_110_WT_NC	9427	35.80%	64.20%	0.00%	remove any remaining N characters
mouse_148_WT_C	8575	35.21%	64.79%	0.00%	remove any remaining N characters
mouse_148_WT_NC	8213	32.38%	67.62%	0.00%	remove any remaining N characters
mouse_158_WT_C	11235	37.46%	62.54%	0.00%	remove any remaining N characters
mouse_158_WT_NC	8894	32.72%	67.28%	0.00%	remove any remaining N characters
mouse_183_KOMIR150_C	7881	31.49%	68.51%	0.00%	remove any remaining N characters
mouse_183_KOMIR150_NC	6252	28.20%	71.80%	0.00%	remove any remaining N characters
mouse_198_KOMIR150_C	8776	34.14%	65.86%	0.00%	remove any remaining N characters
mouse_198_KOMIR150_NC	8884	31.89%	68.11%	0.00%	remove any remaining N characters
mouse_206_KOMIR150_C	5214	31.84%	68.16%	0.00%	remove any remaining N characters
mouse_206_KOMIR150_NC	3455	32.01%	67.99%	0.00%	remove any remaining N characters
mouse_2670_KOTet3_C	8665	37.30%	62.70%	0.00%	remove any remaining N characters
mouse_2670_KOTet3_NC	8420	34.20%	65.80%	0.00%	remove any remaining N characters
mouse_7530_KOTet3_C	8258	36.51%	63.49%	0.00%	remove any remaining N characters
mouse_7530_KOTet3_NC	11296	35.34%	64.66%	0.00%	remove any remaining N characters
mouse_7531_KOTet3_C	9760	41.41%	58.59%	0.00%	remove any remaining N characters
mouse_7532_WT_NC	8689	33.13%	66.87%	0.00%	remove any remaining N characters
mouse_H510_WT_C	7770	32.65%	67.35%	0.00%	remove any remaining N characters
mouse_H510_WT_NC	9069	33.62%	66.38%	0.00%	remove any remaining N characters
mouse_H514_WT_C	7319	35.52%	64.48%	0.00%	remove any remaining N characters
mouse_H514_WT_NC	9942	27.10%	72.90%	0.00%	remove any remaining N characters

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Sort	Group	Column	Description	ID	Scale
\|\|	Total Bp Lost	Total Bp Lost	Total input bps (SE and PE) trimmed.	`Nt_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Nt_%_R2_BP_Lost1`	None
\|\|	% Discarded	% Discarded	Percentage of Reads (SE and PE) Discarded	`Nt_%_Discarded1`	None
\|\|	Notes	Notes	Notes	`Nt_Notes1`	None

NTrimmer: Trimmed Basepairs Composition

Plots the number of N bases trimmed from ends of paired end and single end reads.

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hts_QWindowTrim

Uses a sliding window approach to remove the low quality ends of reads.

Showing ²²/₂₂ rows and ⁵/₅ columns.

Sample Name	% Bp Lost	% R1 of Bp Lost	% R2 of Bp Lost	Avg. Bps Trimmed	Notes
mouse_110_WT_C	0.65%	6.25%	93.75%	1.30	quality trim the ends of reads
mouse_110_WT_NC	0.52%	7.06%	92.94%	1.03	quality trim the ends of reads
mouse_148_WT_C	0.58%	6.15%	93.85%	1.15	quality trim the ends of reads
mouse_148_WT_NC	0.59%	6.32%	93.68%	1.17	quality trim the ends of reads
mouse_158_WT_C	0.49%	7.64%	92.36%	0.97	quality trim the ends of reads
mouse_158_WT_NC	0.56%	6.95%	93.05%	1.12	quality trim the ends of reads
mouse_183_KOMIR150_C	0.59%	5.95%	94.05%	1.18	quality trim the ends of reads
mouse_183_KOMIR150_NC	0.67%	5.82%	94.18%	1.34	quality trim the ends of reads
mouse_198_KOMIR150_C	0.51%	6.90%	93.10%	1.02	quality trim the ends of reads
mouse_198_KOMIR150_NC	0.52%	6.96%	93.04%	1.04	quality trim the ends of reads
mouse_206_KOMIR150_C	0.86%	6.18%	93.82%	1.70	quality trim the ends of reads
mouse_206_KOMIR150_NC	1.00%	5.50%	94.50%	1.98	quality trim the ends of reads
mouse_2670_KOTet3_C	0.53%	7.12%	92.88%	1.05	quality trim the ends of reads
mouse_2670_KOTet3_NC	0.49%	7.83%	92.17%	0.97	quality trim the ends of reads
mouse_7530_KOTet3_C	0.59%	6.32%	93.68%	1.17	quality trim the ends of reads
mouse_7530_KOTet3_NC	0.50%	8.10%	91.90%	1.00	quality trim the ends of reads
mouse_7531_KOTet3_C	0.58%	6.52%	93.48%	1.16	quality trim the ends of reads
mouse_7532_WT_NC	0.52%	7.08%	92.92%	1.04	quality trim the ends of reads
mouse_H510_WT_C	0.57%	6.79%	93.21%	1.14	quality trim the ends of reads
mouse_H510_WT_NC	0.46%	7.96%	92.04%	0.91	quality trim the ends of reads
mouse_H514_WT_C	0.61%	6.14%	93.86%	1.21	quality trim the ends of reads
mouse_H514_WT_NC	0.58%	6.48%	93.52%	1.16	quality trim the ends of reads

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Sort	Group	Column	Description	ID	Scale
\|\|	% Bp Lost	% Bp Lost	Percentage of Input bps (SE and PE) trimmed.	`Qt_%_BP_Lost1`	None
\|\|	% Bp Lost from R1	% R1 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% R2 of Bp Lost	Percentage of total trimmed bps.	`Qt_%_R2_BP_Lost1`	None
\|\|	Avg. Bpss Trimmed	Avg. Bps Trimmed	Average Number of Basepairs Trimmed per Read	`Qt_Avg_BP_Trimmed1`	None
\|\|	Notes	Notes	Notes	`Qt_Notes1`	None

QWindowTrim: Trimmed Basepairs Composition

Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

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hts_LengthFilter

Discards reads below a minimum length threshold.

Showing ²²/₂₂ rows and ²/₂ columns.

Sample Name	% PE Lost	Notes
mouse_110_WT_C	1.27%	remove reads < 50bp
mouse_110_WT_NC	0.97%	remove reads < 50bp
mouse_148_WT_C	1.07%	remove reads < 50bp
mouse_148_WT_NC	1.15%	remove reads < 50bp
mouse_158_WT_C	0.85%	remove reads < 50bp
mouse_158_WT_NC	1.06%	remove reads < 50bp
mouse_183_KOMIR150_C	1.10%	remove reads < 50bp
mouse_183_KOMIR150_NC	1.39%	remove reads < 50bp
mouse_198_KOMIR150_C	0.95%	remove reads < 50bp
mouse_198_KOMIR150_NC	0.95%	remove reads < 50bp
mouse_206_KOMIR150_C	1.69%	remove reads < 50bp
mouse_206_KOMIR150_NC	2.35%	remove reads < 50bp
mouse_2670_KOTet3_C	0.96%	remove reads < 50bp
mouse_2670_KOTet3_NC	0.88%	remove reads < 50bp
mouse_7530_KOTet3_C	1.09%	remove reads < 50bp
mouse_7530_KOTet3_NC	0.92%	remove reads < 50bp
mouse_7531_KOTet3_C	1.08%	remove reads < 50bp
mouse_7532_WT_NC	0.96%	remove reads < 50bp
mouse_H510_WT_C	1.07%	remove reads < 50bp
mouse_H510_WT_NC	0.85%	remove reads < 50bp
mouse_H514_WT_C	1.32%	remove reads < 50bp
mouse_H514_WT_NC	1.07%	remove reads < 50bp

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|		% PE Lost	% PE Lost	Percentage of Paired End Reads Lost	`Lf_PE_loss1`	None
\|\|		Notes	Notes	Notes	`Lf_Notes1`	None

hts_Stats 2

Generates a JSON formatted file containing a set of statistical measures about the input read data.

Showing ²²/₂₂ rows and ⁶/₆ columns.

Sample Name	% PE	% R1 Q30	% R2 Q30	GC Content	N Content	Notes
mouse_110_WT_C	100.00%	95.91%	93.29%	50.22%	0.0000%	final stats
mouse_110_WT_NC	100.00%	96.16%	94.53%	50.26%	0.0000%	final stats
mouse_148_WT_C	100.00%	96.11%	94.12%	49.93%	0.0000%	final stats
mouse_148_WT_NC	100.00%	96.10%	94.15%	50.17%	0.0000%	final stats
mouse_158_WT_C	100.00%	95.80%	94.15%	50.01%	0.0000%	final stats
mouse_158_WT_NC	100.00%	95.91%	93.77%	50.22%	0.0000%	final stats
mouse_183_KOMIR150_C	100.00%	96.32%	94.41%	50.20%	0.0000%	final stats
mouse_183_KOMIR150_NC	100.00%	96.03%	93.43%	50.41%	0.0000%	final stats
mouse_198_KOMIR150_C	100.00%	96.25%	94.62%	50.25%	0.0000%	final stats
mouse_198_KOMIR150_NC	100.00%	95.97%	93.96%	50.36%	0.0000%	final stats
mouse_206_KOMIR150_C	100.00%	95.23%	92.27%	50.02%	0.0000%	final stats
mouse_206_KOMIR150_NC	100.00%	95.13%	91.85%	50.23%	0.0000%	final stats
mouse_2670_KOTet3_C	100.00%	95.95%	94.13%	50.05%	0.0000%	final stats
mouse_2670_KOTet3_NC	100.00%	95.85%	94.15%	50.02%	0.0000%	final stats
mouse_7530_KOTet3_C	100.00%	96.13%	94.16%	49.88%	0.0000%	final stats
mouse_7530_KOTet3_NC	100.00%	95.44%	93.09%	49.84%	0.0000%	final stats
mouse_7531_KOTet3_C	100.00%	95.87%	93.26%	49.75%	0.0000%	final stats
mouse_7532_WT_NC	100.00%	96.27%	94.62%	49.85%	0.0000%	final stats
mouse_H510_WT_C	100.00%	96.05%	94.07%	49.86%	0.0000%	final stats
mouse_H510_WT_NC	100.00%	96.10%	94.80%	49.78%	0.0000%	final stats
mouse_H514_WT_C	100.00%	96.18%	94.27%	49.83%	0.0000%	final stats
mouse_H514_WT_NC	100.00%	96.06%	93.63%	49.75%	0.0000%	final stats

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Sort	Group	Column	Description	ID	Scale
\|\|	% PE	% PE	percentage of paried end reads	`St_PE_Fraction2`	None
\|\|	% R1 Q30	% R1 Q30	percentage of read 1 bps Q30 or greater	`St_R1_Q302`	None
\|\|	% R2 Q30	% R2 Q30	percentage of read 2 bps Q30 or greater	`St_R2_Q302`	None
\|\|	GC Content	GC Content	Percentage of bps that are G or C	`St_GC_Content2`	None
\|\|	N Content	N Content	Percentage of bps that are N	`St_N_Content2`	None
\|\|	Notes	Notes	Notes	`St_Notes2`	None

Read Lengths: Paired End

Distribution of read lengths for each sample.

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Base by Cycle: Paired End

Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

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Quality by Cycle: Paired End

Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

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Table Ephb: Columns

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Table Tqgx: Columns

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Table Gzuh: Columns

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Table Cpbi: Columns

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Table Kjwz: Columns

SuperDeduper: Duplicate Saturation

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Table Gerb: Columns

AdapterTrimmer: Trimmed Basepairs Composition

hts_PolyATTrim

Table Newo: Columns

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Table Knrq: Columns

NTrimmer: Trimmed Basepairs Composition

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Table Ugyp: Columns

QWindowTrim: Trimmed Basepairs Composition

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Table Agbx: Columns

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Table Nmcl: Columns

Read Lengths: Paired End

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