HTSMultiQC-cleaning-report: MultiQC Report

Processing Overview

General statistics from the HTStream pipeline.

Preprocessing Statistics

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Fragment Reduction

Showing ²²/₂₂ rows and ⁷/₇ columns.

Sample Name	Pipeline Input	hts_Stats_1	hts_SeqScreener_1	hts_SeqScreener_2	hts_SuperDeduper_1	hts_LengthFilter_1	hts_Stats_2
mouse_110_WT_C	5000000	5000000	4999985	4999985	3089029	3049794	3049794
mouse_110_WT_NC	5000000	5000000	4999986	4999986	3729279	3693198	3693198
mouse_148_WT_C	5000000	5000000	4999989	4999989	3669765	3630693	3630693
mouse_148_WT_NC	5000000	5000000	4999988	4999988	3465048	3425112	3425112
mouse_158_WT_C	5000000	5000000	4999990	4999990	3895837	3862642	3862642
mouse_158_WT_NC	5000000	5000000	4999992	4999992	3563187	3525523	3525523
mouse_183_KOMIR150_C	5000000	5000000	4999987	4999987	3361523	3324635	3324635
mouse_183_KOMIR150_NC	5000000	5000000	4999982	4999982	2542175	2506784	2506784
mouse_198_KOMIR150_C	5000000	5000000	4999986	4999986	3649690	3614911	3614911
mouse_198_KOMIR150_NC	5000000	5000000	4999984	4999984	3762565	3726853	3726853
mouse_206_KOMIR150_C	5000000	5000000	4999968	4999968	1947522	1914654	1914654
mouse_206_KOMIR150_NC	5000000	5000000	4999975	4999975	1407841	1374828	1374828
mouse_2670_KOTet3_C	5000000	5000000	4999984	4999984	3813041	3776609	3776609
mouse_2670_KOTet3_NC	5000000	5000000	4999986	4999986	3876015	3841901	3841901
mouse_7530_KOTet3_C	5000000	5000000	4999981	4999981	3526428	3488016	3488016
mouse_7530_KOTet3_NC	5000000	5000000	4999989	4999989	3948759	3912583	3912583
mouse_7531_KOTet3_C	5000000	5000000	4999993	4999993	3703647	3663752	3663752
mouse_7532_WT_NC	5000000	5000000	4999985	4999985	3775028	3738835	3738835
mouse_H510_WT_C	5000000	5000000	4999989	4999989	3527799	3489938	3489938
mouse_H510_WT_NC	5000000	5000000	4999983	4999983	3880241	3847419	3847419
mouse_H514_WT_C	5000000	5000000	4999986	4999986	3235510	3192819	3192819
mouse_H514_WT_NC	5000000	5000000	4999986	4999986	3750453	3710385	3710385

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Sort	Group	Column	Description	ID	Scale
\|\|	Pipeline Input	Pipeline Input	Number of Output Fragments for Pipeline Input	`Pipeline Input (read)`	None
\|\|	hts_Stats_1	hts_Stats_1	Number of Output Fragments for hts_Stats_1	`hts_Stats_1 (read)`	None
\|\|	hts_SeqScreener_1	hts_SeqScreener_1	Number of Output Fragments for hts_SeqScreener_1	`hts_SeqScreener_1 (read)`	None
\|\|	hts_SeqScreener_2	hts_SeqScreener_2	Number of Output Fragments for hts_SeqScreener_2	`hts_SeqScreener_2 (read)`	None
\|\|	hts_SuperDeduper_1	hts_SuperDeduper_1	Number of Output Fragments for hts_SuperDeduper_1	`hts_SuperDeduper_1 (read)`	None
\|\|	hts_LengthFilter_1	hts_LengthFilter_1	Number of Output Fragments for hts_LengthFilter_1	`hts_LengthFilter_1 (read)`	None
\|\|	hts_Stats_2	hts_Stats_2	Number of Output Fragments for hts_Stats_2	`hts_Stats_2 (read)`	None

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Basepair Reduction

Showing ²²/₂₂ rows and ⁷/₇ columns.

Sample Name	Pipeline Input	hts_Stats_1	hts_AdapterTrimmer_1	hts_PolyATTrim_1	hts_NTrimmer_1	hts_QWindowTrim_1	hts_Stats_2
mouse_110_WT_C	1010000000	1010000000	615125056	615064074	615057161	611049368	606844812
mouse_110_WT_NC	1010000000	1010000000	743111268	743041739	743032308	739181927	735151141
mouse_148_WT_C	1010000000	1010000000	732461798	732390262	732381689	728162177	723727337
mouse_148_WT_NC	1010000000	1010000000	690150184	690085577	690077366	686030273	681684297
mouse_158_WT_C	1010000000	1010000000	778844318	778773360	778762127	774986560	771187682
mouse_158_WT_NC	1010000000	1010000000	711542248	711477809	711468914	707474676	703325461
mouse_183_KOMIR150_C	1010000000	1010000000	671089122	671029420	671021532	667068126	662877880
mouse_183_KOMIR150_NC	1010000000	1010000000	506719490	506671853	506665599	503269432	499627821
mouse_198_KOMIR150_C	1010000000	1010000000	728388186	728321824	728313046	724581432	720706600
mouse_198_KOMIR150_NC	1010000000	1010000000	751433602	751365846	751356962	747457443	743452406
mouse_206_KOMIR150_C	1010000000	1010000000	387283588	387243476	387238260	383925166	380619238
mouse_206_KOMIR150_NC	1010000000	1010000000	278509184	278477946	278474490	275689298	272546031
mouse_2670_KOTet3_C	1010000000	1010000000	760694318	760626935	760618267	756624645	752498633
mouse_2670_KOTet3_NC	1010000000	1010000000	774096618	774024491	774016070	770260175	766445083
mouse_7530_KOTet3_C	1010000000	1010000000	702945124	702878069	702869809	698742857	694413160
mouse_7530_KOTet3_NC	1010000000	1010000000	788203882	788129988	788118690	784168179	780182278
mouse_7531_KOTet3_C	1010000000	1010000000	738424992	738350729	738340967	734043665	729593332
mouse_7532_WT_NC	1010000000	1010000000	752813198	752739913	752731225	748791718	744662748
mouse_H510_WT_C	1010000000	1010000000	703365704	703299641	703291861	699282166	695080677
mouse_H510_WT_NC	1010000000	1010000000	775250838	775179945	775170876	771635383	767986652
mouse_H514_WT_C	1010000000	1010000000	642373506	642311274	642303942	638392350	633968202
mouse_H514_WT_NC	1010000000	1010000000	748802480	748725923	748715973	744367409	739845151

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Sort	Group	Column	Description	ID	Scale
\|\|	Pipeline Input	Pipeline Input	Number of Output Bps for Pipeline Input	`Pipeline Input (bps)`	None
\|\|	hts_Stats_1	hts_Stats_1	Number of Output Bps for hts_Stats_1	`hts_Stats_1 (bps)`	None
\|\|	hts_AdapterTrimmer_1	hts_AdapterTrimmer_1	Number of Output Bps for hts_AdapterTrimmer_1	`hts_AdapterTrimmer_1 (bps)`	None
\|\|	hts_PolyATTrim_1	hts_PolyATTrim_1	Number of Output Bps for hts_PolyATTrim_1	`hts_PolyATTrim_1 (bps)`	None
\|\|	hts_NTrimmer_1	hts_NTrimmer_1	Number of Output Bps for hts_NTrimmer_1	`hts_NTrimmer_1 (bps)`	None
\|\|	hts_QWindowTrim_1	hts_QWindowTrim_1	Number of Output Bps for hts_QWindowTrim_1	`hts_QWindowTrim_1 (bps)`	None
\|\|	hts_Stats_2	hts_Stats_2	Number of Output Bps for hts_Stats_2	`hts_Stats_2 (bps)`	None

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hts_Stats 1

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 Length Histogram: Paried End

Base by Cycle: Paired End

Sample Checks:

mouse_110_WT_C

mouse_110_WT_NC

mouse_148_WT_C

mouse_148_WT_NC

mouse_158_WT_C

mouse_158_WT_NC

mouse_183_KOMIR150_C

mouse_183_KOMIR150_NC

mouse_198_KOMIR150_C

mouse_198_KOMIR150_NC

mouse_206_KOMIR150_C

mouse_206_KOMIR150_NC

mouse_2670_KOTet3_C

mouse_2670_KOTet3_NC

mouse_7530_KOTet3_C

mouse_7530_KOTet3_NC

mouse_7531_KOTet3_C

mouse_7532_WT_NC

mouse_H510_WT_C

mouse_H510_WT_NC

mouse_H514_WT_C

mouse_H514_WT_NC

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Quality by Cycle: Paired End

Sample Checks:

mouse_110_WT_C

mouse_110_WT_NC

mouse_148_WT_C

mouse_148_WT_NC

mouse_158_WT_C

mouse_158_WT_NC

mouse_183_KOMIR150_C

mouse_183_KOMIR150_NC

mouse_198_KOMIR150_C

mouse_198_KOMIR150_NC

mouse_206_KOMIR150_C

mouse_206_KOMIR150_NC

mouse_2670_KOTet3_C

mouse_2670_KOTet3_NC

mouse_7530_KOTet3_C

mouse_7530_KOTet3_NC

mouse_7531_KOTet3_C

mouse_7532_WT_NC

mouse_H510_WT_C

mouse_H510_WT_NC

mouse_H514_WT_C

mouse_H514_WT_NC

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hts_SeqScreener 1

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 1

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

Duplicate Saturation

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hts_AdapterTrimmer 1

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

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hts_PolyATTrim 1

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

Showing ²²/₂₂ rows and ⁵/₅ columns.

Sample Name	Total Bp Lost	% Bp Lost from R1	% Bp Lost from R2	% Bp Lost from SE	Notes
mouse_110_WT_C	60982	0.00%	100.00%	0.00%	remove polyA
mouse_110_WT_NC	69529	0.00%	100.00%	0.00%	remove polyA
mouse_148_WT_C	71536	0.00%	100.00%	0.00%	remove polyA
mouse_148_WT_NC	64607	0.00%	100.00%	0.00%	remove polyA
mouse_158_WT_C	70958	0.00%	100.00%	0.00%	remove polyA
mouse_158_WT_NC	64439	0.00%	100.00%	0.00%	remove polyA
mouse_183_KOMIR150_C	59702	0.00%	100.00%	0.00%	remove polyA
mouse_183_KOMIR150_NC	47637	0.00%	100.00%	0.00%	remove polyA
mouse_198_KOMIR150_C	66362	0.00%	100.00%	0.00%	remove polyA
mouse_198_KOMIR150_NC	67756	0.00%	100.00%	0.00%	remove polyA
mouse_206_KOMIR150_C	40112	0.00%	100.00%	0.00%	remove polyA
mouse_206_KOMIR150_NC	31238	0.00%	100.00%	0.00%	remove polyA
mouse_2670_KOTet3_C	67383	0.00%	100.00%	0.00%	remove polyA
mouse_2670_KOTet3_NC	72127	0.00%	100.00%	0.00%	remove polyA
mouse_7530_KOTet3_C	67055	0.00%	100.00%	0.00%	remove polyA
mouse_7530_KOTet3_NC	73894	0.00%	100.00%	0.00%	remove polyA
mouse_7531_KOTet3_C	74263	0.00%	100.00%	0.00%	remove polyA
mouse_7532_WT_NC	73285	0.00%	100.00%	0.00%	remove polyA
mouse_H510_WT_C	66063	0.00%	100.00%	0.00%	remove polyA
mouse_H510_WT_NC	70893	0.00%	100.00%	0.00%	remove polyA
mouse_H514_WT_C	62232	0.00%	100.00%	0.00%	remove polyA
mouse_H514_WT_NC	76557	0.00%	100.00%	0.00%	remove polyA

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	Total Bp Lost	Total Bp Lost	Total input bps (SE and PE) trimmed.	`Pt_BP_Lost1`	None
\|\|	% Bp Lost from R1	% Bp Lost from R1	Percentage of Input bps (SE and PE) trimmed.	`Pt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% Bp Lost from R2	Percentage of Input bps (SE and PE) trimmed.	`Pt_%_R2_BP_Lost1`	None
\|\|	% Bp Lost from SE	% Bp Lost from SE	Percentage of Input bps (SE and PE) trimmed.	`Pt_%_SE_BP_Lost1`	None
\|\|	Notes	Notes	Notes	`Pt_Notes1`	None

hts_NTrimmer 1

Trims reads to the longest subsequence that contains no Ns.

Showing ²²/₂₂ rows and ⁶/₆ columns.

Sample Name	Total Bp Lost	% Bp Lost from R1	% Bp Lost from R2	% Bp Lost from SE	% Discarded	Notes
mouse_110_WT_C	6913	34.31%	65.69%	0.00%	0.00%	remove any remaining N characters
mouse_110_WT_NC	9431	35.87%	64.13%	0.00%	0.00%	remove any remaining N characters
mouse_148_WT_C	8573	35.25%	64.75%	0.00%	0.00%	remove any remaining N characters
mouse_148_WT_NC	8211	32.42%	67.58%	0.00%	0.00%	remove any remaining N characters
mouse_158_WT_C	11233	37.51%	62.49%	0.00%	0.00%	remove any remaining N characters
mouse_158_WT_NC	8895	32.76%	67.24%	0.00%	0.00%	remove any remaining N characters
mouse_183_KOMIR150_C	7888	31.54%	68.46%	0.00%	0.00%	remove any remaining N characters
mouse_183_KOMIR150_NC	6254	28.21%	71.79%	0.00%	0.00%	remove any remaining N characters
mouse_198_KOMIR150_C	8778	34.20%	65.80%	0.00%	0.00%	remove any remaining N characters
mouse_198_KOMIR150_NC	8884	31.92%	68.08%	0.00%	0.00%	remove any remaining N characters
mouse_206_KOMIR150_C	5216	31.84%	68.16%	0.00%	0.00%	remove any remaining N characters
mouse_206_KOMIR150_NC	3456	32.03%	67.97%	0.00%	0.00%	remove any remaining N characters
mouse_2670_KOTet3_C	8668	37.32%	62.68%	0.00%	0.00%	remove any remaining N characters
mouse_2670_KOTet3_NC	8421	34.22%	65.78%	0.00%	0.00%	remove any remaining N characters
mouse_7530_KOTet3_C	8260	36.53%	63.47%	0.00%	0.00%	remove any remaining N characters
mouse_7530_KOTet3_NC	11298	35.37%	64.63%	0.00%	0.00%	remove any remaining N characters
mouse_7531_KOTet3_C	9762	41.46%	58.54%	0.00%	0.00%	remove any remaining N characters
mouse_7532_WT_NC	8688	33.17%	66.83%	0.00%	0.00%	remove any remaining N characters
mouse_H510_WT_C	7780	32.75%	67.25%	0.00%	0.00%	remove any remaining N characters
mouse_H510_WT_NC	9069	33.64%	66.36%	0.00%	0.00%	remove any remaining N characters
mouse_H514_WT_C	7332	35.73%	64.27%	0.00%	0.00%	remove any remaining N characters
mouse_H514_WT_NC	9950	27.15%	72.85%	0.00%	0.00%	remove any remaining N characters

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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	% Bp Lost from R1	Percentage of Input bps (SE and PE) trimmed.	`Nt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% Bp Lost from R2	Percentage of Input bps (SE and PE) trimmed.	`Nt_%_R2_BP_Lost1`	None
\|\|	% Bp Lost from SE	% Bp Lost from SE	Percentage of Input bps (SE and PE) trimmed.	`Nt_%_SE_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

loading..

hts_QWindowTrim 1

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	% Bp Lost from R1	% Bp Lost from R2	Avg. Bps Trimmed	Notes
mouse_110_WT_C	0.65%	6.22%	93.78%	1.30	quality trim the ends of reads
mouse_110_WT_NC	0.52%	7.02%	92.98%	1.03	quality trim the ends of reads
mouse_148_WT_C	0.58%	6.11%	93.89%	1.15	quality trim the ends of reads
mouse_148_WT_NC	0.59%	6.29%	93.71%	1.17	quality trim the ends of reads
mouse_158_WT_C	0.48%	7.59%	92.41%	0.97	quality trim the ends of reads
mouse_158_WT_NC	0.56%	6.92%	93.08%	1.12	quality trim the ends of reads
mouse_183_KOMIR150_C	0.59%	5.91%	94.09%	1.18	quality trim the ends of reads
mouse_183_KOMIR150_NC	0.67%	5.78%	94.22%	1.34	quality trim the ends of reads
mouse_198_KOMIR150_C	0.51%	6.86%	93.14%	1.02	quality trim the ends of reads
mouse_198_KOMIR150_NC	0.52%	6.92%	93.08%	1.04	quality trim the ends of reads
mouse_206_KOMIR150_C	0.86%	6.15%	93.85%	1.70	quality trim the ends of reads
mouse_206_KOMIR150_NC	1.00%	5.48%	94.52%	1.98	quality trim the ends of reads
mouse_2670_KOTet3_C	0.53%	7.07%	92.93%	1.05	quality trim the ends of reads
mouse_2670_KOTet3_NC	0.49%	7.79%	92.21%	0.97	quality trim the ends of reads
mouse_7530_KOTet3_C	0.59%	6.28%	93.72%	1.17	quality trim the ends of reads
mouse_7530_KOTet3_NC	0.50%	8.04%	91.96%	1.00	quality trim the ends of reads
mouse_7531_KOTet3_C	0.58%	6.48%	93.52%	1.16	quality trim the ends of reads
mouse_7532_WT_NC	0.52%	7.03%	92.97%	1.04	quality trim the ends of reads
mouse_H510_WT_C	0.57%	6.75%	93.25%	1.14	quality trim the ends of reads
mouse_H510_WT_NC	0.46%	7.92%	92.08%	0.91	quality trim the ends of reads
mouse_H514_WT_C	0.61%	6.10%	93.90%	1.21	quality trim the ends of reads
mouse_H514_WT_NC	0.58%	6.44%	93.56%	1.16	quality trim the ends of reads

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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	% Bp Lost from R1	Percentage of Input bps (SE and PE) trimmed.	`Qt_%_R1_BP_Lost1`	None
\|\|	% Bp Lost from R2	% Bp Lost from R2	Percentage of Input bps (SE and PE) trimmed.	`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

loading..

hts_LengthFilter 1

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	1.06%	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	2.34%	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

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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%	50.20%	0.0000%	final stats
mouse_110_WT_NC	100.00%	96.15%	94.53%	50.24%	0.0000%	final stats
mouse_148_WT_C	100.00%	96.11%	94.12%	49.91%	0.0000%	final stats
mouse_148_WT_NC	100.00%	96.10%	94.15%	50.16%	0.0000%	final stats
mouse_158_WT_C	100.00%	95.80%	94.15%	49.99%	0.0000%	final stats
mouse_158_WT_NC	100.00%	95.91%	93.77%	50.20%	0.0000%	final stats
mouse_183_KOMIR150_C	100.00%	96.32%	94.41%	50.18%	0.0000%	final stats
mouse_183_KOMIR150_NC	100.00%	96.03%	93.43%	50.39%	0.0000%	final stats
mouse_198_KOMIR150_C	100.00%	96.25%	94.62%	50.23%	0.0000%	final stats
mouse_198_KOMIR150_NC	100.00%	95.97%	93.96%	50.34%	0.0000%	final stats
mouse_206_KOMIR150_C	100.00%	95.23%	92.27%	50.00%	0.0000%	final stats
mouse_206_KOMIR150_NC	100.00%	95.13%	91.85%	50.21%	0.0000%	final stats
mouse_2670_KOTet3_C	100.00%	95.95%	94.13%	50.03%	0.0000%	final stats
mouse_2670_KOTet3_NC	100.00%	95.85%	94.15%	50.00%	0.0000%	final stats
mouse_7530_KOTet3_C	100.00%	96.13%	94.16%	49.86%	0.0000%	final stats
mouse_7530_KOTet3_NC	100.00%	95.44%	93.08%	49.83%	0.0000%	final stats
mouse_7531_KOTet3_C	100.00%	95.86%	93.26%	49.73%	0.0000%	final stats
mouse_7532_WT_NC	100.00%	96.26%	94.62%	49.83%	0.0000%	final stats
mouse_H510_WT_C	100.00%	96.05%	94.07%	49.84%	0.0000%	final stats
mouse_H510_WT_NC	100.00%	96.10%	94.80%	49.76%	0.0000%	final stats
mouse_H514_WT_C	100.00%	96.18%	94.27%	49.82%	0.0000%	final stats
mouse_H514_WT_NC	100.00%	96.06%	93.63%	49.73%	0.0000%	final stats

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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 Length Histogram: Paried End

Base by Cycle: Paired End

Sample Checks:

mouse_110_WT_C

mouse_110_WT_NC

mouse_148_WT_C

mouse_148_WT_NC

mouse_158_WT_C

mouse_158_WT_NC

mouse_183_KOMIR150_C

mouse_183_KOMIR150_NC

mouse_198_KOMIR150_C

mouse_198_KOMIR150_NC

mouse_206_KOMIR150_C

mouse_206_KOMIR150_NC

mouse_2670_KOTet3_C

mouse_2670_KOTet3_NC

mouse_7530_KOTet3_C

mouse_7530_KOTet3_NC

mouse_7531_KOTet3_C

mouse_7532_WT_NC

mouse_H510_WT_C

mouse_H510_WT_NC

mouse_H514_WT_C

mouse_H514_WT_NC

loading..

Quality by Cycle: Paired End

Sample Checks:

mouse_110_WT_C

mouse_110_WT_NC

mouse_148_WT_C

mouse_148_WT_NC

mouse_158_WT_C

mouse_158_WT_NC

mouse_183_KOMIR150_C

mouse_183_KOMIR150_NC

mouse_198_KOMIR150_C

mouse_198_KOMIR150_NC

mouse_206_KOMIR150_C

mouse_206_KOMIR150_NC

mouse_2670_KOTet3_C

mouse_2670_KOTet3_NC

mouse_7530_KOTet3_C

mouse_7530_KOTet3_NC

mouse_7531_KOTet3_C

mouse_7532_WT_NC

mouse_H510_WT_C

mouse_H510_WT_NC

mouse_H514_WT_C

mouse_H514_WT_NC

loading..

v1.10.dev0

HTSMultiQC-cleaning-report

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Preprocessing Statistics

Fragment Reduction

Basepair Reduction

hts_Stats 1

Read Length Histogram: Paried End

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener 1

hts_SeqScreener 2

hts_SuperDeduper 1

Duplicate Saturation

hts_AdapterTrimmer 1

AdapterTrimmer Trimmed Basepairs Composition

hts_PolyATTrim 1

hts_NTrimmer 1

NTrimmer Trimmed Basepairs Composition

hts_QWindowTrim 1

QWindowTrim Trimmed Basepairs Composition

hts_LengthFilter 1

hts_Stats 2

Read Length Histogram: Paried End

Base by Cycle: Paired End

Quality by Cycle: Paired End

Toggle navigation v1.10.dev0

HTSMultiQC-cleaning-report

MultiQC Toolbox

Apply Highlight Samples

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About MultiQC

HTSMultiQC-cleaning-report

HTStream

Processing Overview

Preprocessing Statistics

Fragment Reduction

Fragment Reduction: Columns

Basepair Reduction

Basepair Reduction: Columns

hts_Stats 1

Table Splf: Columns

Read Length Histogram: Paried End

Base by Cycle: Paired End

Quality by Cycle: Paired End

hts_SeqScreener 1

Table Xqun: Columns

hts_SeqScreener 2

Table Iwyf: Columns

hts_SuperDeduper 1

Table Wgnp: Columns

Duplicate Saturation

hts_AdapterTrimmer 1

Table Otfn: Columns

AdapterTrimmer Trimmed Basepairs Composition

hts_PolyATTrim 1

Table Jrds: Columns

hts_NTrimmer 1

Table Anis: Columns

NTrimmer Trimmed Basepairs Composition

hts_QWindowTrim 1

Table Chgl: Columns

QWindowTrim Trimmed Basepairs Composition

hts_LengthFilter 1

Table Mosk: Columns

hts_Stats 2

Table Psml: Columns

Read Length Histogram: Paried End

Base by Cycle: Paired End

Quality by Cycle: Paired End

v1.10.dev0

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