JM101_3_CGATGT_L005_R1_001.fastq FastQC Report

Basic Statistics

Measure	Value
Filename	JM101_3_CGATGT_L005_R1_001.fastq
File type	Conventional base calls
Encoding	Sanger / Illumina 1.9
Total Sequences	10574364
Sequences flagged as poor quality	0
Sequence length	50
%GC	52

Per base sequence quality

Per base quality graph

Per tile sequence quality

Per base quality graph

Per sequence quality scores

Per Sequence quality graph

Per base sequence content

Per sequence GC content

Per sequence GC content graph

Per base N content

N content graph

Sequence Length Distribution

Sequence length distribution

Sequence Duplication Levels

Duplication level graph

Overrepresented sequences

Sequence	Count	Percentage	Possible Source
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGC	4509560	42.646158199207065	RNA PCR Primer, Index 2 (100% over 50bp)
TGGAGTGTGACAATGGTGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCA	263538	2.492234993991128	RNA PCR Primer, Index 1 (100% over 28bp)
AAGCTGCCAGCTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	122022	1.1539417406096482	RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGG	116325	1.1000661600073536	No Hit
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	113189	1.0704095300672456	RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	103907	0.982631201271301	RNA PCR Primer, Index 1 (100% over 29bp)
TAGCTTATCAGACTGGTGTTGGCTGGAATTCTCGGGTGCCAAGGAACTCC	99213	0.9382408246964072	RNA PCR Primer, Index 1 (100% over 27bp)
GTTCTACAGTCCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	90283	0.8537913013019033	RNA PCR Primer, Index 2 (100% over 35bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	82299	0.7782879424237713	RNA PCR Primer, Index 2 (100% over 35bp)
ATGACCTATGAATTGACAGCCATGGAATTCTCGGGTGCCAAGGAACTCCA	80553	0.7617763110859433	RNA PCR Primer, Index 1 (100% over 28bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC	75056	0.7097920971890129	RNA PCR Primer, Index 1 (100% over 27bp)
TGGAGTGTGACAATGGTGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCC	74998	0.7092436008444574	RNA PCR Primer, Index 1 (100% over 27bp)
ATGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG	74807	0.7074373456408348	RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	64872	0.6134837045518765	RNA PCR Primer, Index 1 (100% over 28bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA	62648	0.5924517067882286	RNA PCR Primer, Index 1 (100% over 28bp)
CTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	60518	0.5723086513761017	RNA PCR Primer, Index 2 (100% over 34bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	56227	0.5317293787125165	RNA PCR Primer, Index 1 (100% over 28bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	56172	0.5312092528685414	RNA PCR Primer, Index 2 (100% over 34bp)
AGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGT	55058	0.5206743403196636	RNA PCR Primer, Index 1 (100% over 30bp)
CCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	47211	0.44646656763470594	RNA PCR Primer, Index 1 (100% over 33bp)
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTAT	45416	0.4294915514540638	RNA PCR Primer, Index 2 (100% over 48bp)
TCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	43023	0.4068613488243832	RNA PCR Primer, Index 1 (100% over 33bp)
TAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAG	41704	0.3943877854025074	RNA PCR Primer, Index 1 (100% over 29bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGGATCTCGTATGC	38121	0.3605039508759108	RNA PCR Primer, Index 2 (98% over 50bp)
TGGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC	36555	0.34569454957291046	RNA PCR Primer, Index 1 (100% over 33bp)
ACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	35960	0.3400677336244525	RNA PCR Primer, Index 2 (100% over 36bp)
TTCAAGTAATCCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	33805	0.31968825737415507	RNA PCR Primer, Index 1 (100% over 28bp)
CAGAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCC	32931	0.31142298487171427	RNA PCR Primer, Index 1 (100% over 27bp)
AGAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCA	32135	0.3038953453843654	RNA PCR Primer, Index 1 (100% over 28bp)
TTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	31751	0.30026392131006646	RNA PCR Primer, Index 1 (100% over 32bp)
TGAGGTAGTAGTTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	31100	0.2941075226841066	RNA PCR Primer, Index 1 (100% over 28bp)
GGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	30707	0.29039098710806627	RNA PCR Primer, Index 2 (100% over 34bp)
TACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	30476	0.2882064585633708	RNA PCR Primer, Index 2 (100% over 35bp)
TAACGGAACCCATAATGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC	30237	0.2859462753504608	RNA PCR Primer, Index 1 (100% over 27bp)
GTTCTACAGTCCGACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC	27987	0.2646683999151155	RNA PCR Primer, Index 2 (100% over 34bp)
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC	27846	0.2633349863878338	No Hit
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC	26675	0.2522610343279274	RNA PCR Primer, Index 1 (100% over 26bp)
TAGCAGCACGTAAATATTGGAGTGGAATTCTCGGGTGCCAAGGAACTCCA	26080	0.24663421837946947	RNA PCR Primer, Index 1 (100% over 28bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC	25908	0.24500764301285638	RNA PCR Primer, Index 1 (100% over 26bp)
AACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT	23518	0.22240581088375624	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA	23120	0.2186419911400818	No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTCTGCCTTGGAATTCTCGGGTGCC	22945	0.2169870452728883	No Hit
GCATCGATGGTTCAGTGGTAGAATGCTCGCCTTGGAATTCTCGGGTGCCA	22455	0.21235319684474643	No Hit
TGAGAACTGAATTCCATAGATGGTGGAATTCTCGGGTGCCAAGGAACTCC	21078	0.19933113707831504	RNA PCR Primer, Index 1 (100% over 27bp)
GCATCGATGGTTCAGTGGTAGAATGCTGGAATTCTCGGGTGCCAAGGAAC	19534	0.18472978611290475	RNA PCR Primer, Index 1 (100% over 24bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC	18942	0.17913134066502723	No Hit
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGGAATTCTCGGGTGCCAA	18502	0.17497033391322636	No Hit
TAGCTTATCAGACTGGTGTTGGTGGAATTCTCGGGTGCCAAGGAACTCCA	18252	0.17260612553152133	RNA PCR Primer, Index 1 (100% over 28bp)
GATCCATGATGACATTAAAACATAACGTGACTGTTGGATGAAGCTTGCGG	17472	0.16522979538060162	No Hit
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTTGGAATTCTCGGGTGCC	16361	0.15472325333230444	No Hit
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGTTGTATCTCGTATGC	16221	0.1533992966385496	RNA PCR Primer, Index 2 (98% over 50bp)
CTGGACAACTCTTAGCGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA	15932	0.15066627174929859	RNA PCR Primer, Index 1 (100% over 32bp)
TGAGGTAGTAGATTGAATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	15318	0.144859775963831	RNA PCR Primer, Index 1 (100% over 28bp)
AGCCTGTGATGATACAAGTTATCCCTGTCTGAACTCTGGTGTGGAATTCT	15210	0.14383843794293444	No Hit
AACATTCAACGCTGTCGGTGATGGAATTCTCGGGTGCCAAGGAACTCCAG	14567	0.13775769398518908	RNA PCR Primer, Index 1 (100% over 29bp)
TGAGGTAGTAGTTTGTGCTGTTTGGAATTCTCGGGTGCCAAGGAACTCCA	14499	0.1371146293053653	RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGTTAAGTTCTGCCTGGAATTCTCGGGTGCCAAGGAACTCCA	14002	0.1324145830425357	RNA PCR Primer, Index 1 (100% over 28bp)
GCATCGATGGTTCAGTGGTAGAATGCTCTGGAATTCTCGGGTGCCAAGGA	13499	0.12765779577854516	RNA PCR Primer, Index 1 (100% over 22bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG	13360	0.12634329591831717	RNA PCR Primer, Index 1 (100% over 29bp)
TCACAGTGAACCGGTCTCTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	13095	0.12383723503370983	RNA PCR Primer, Index 1 (100% over 29bp)
TCGCTGCGATCCATTGAAAGTCAGCCCTCGATCCAAGTTTTTGTTGGAAT	13007	0.12300503368334965	No Hit
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG	12993	0.12287263801397418	RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCCATTGAAAGTCAGCCCTCGATCCAAGTTTTTGTTGGAA	12797	0.12101909864271743	No Hit
GCATCGATGGTTCAGTGGTAGAATGCTCGCCTGGAATTCTCGGGTGCCAA	12770	0.12076376413749329	No Hit
TGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCG	12688	0.11998830378829403	RNA PCR Primer, Index 2 (100% over 35bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAACGATGTATCTCGTATGC	12542	0.11860760609337828	RNA PCR Primer, Index 2 (98% over 50bp)
GTGGGCTCTGGTAGTCCAGTGGCAAGATCGTCTGACTTACGTTTTGGAAT	12197	0.11534499852662533	No Hit
CAACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC	12033	0.11379407782822683	No Hit
TGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGATGTATCTCGTATGCC	11896	0.11249849163505246	RNA PCR Primer, Index 2 (98% over 50bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTTG	11695	0.11059766809616162	No Hit
TGGACGTGATGAGCAGGTGTTACCGCCCCAGTCTGATGTTTGGTGACTGA	11630	0.10998297391691832	No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA	11611	0.10980329407990874	RNA PCR Primer, Index 1 (100% over 28bp)
ACAGTAGTCTGCACATTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG	11204	0.10595436283449293	RNA PCR Primer, Index 1 (100% over 29bp)
CCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCGA	10946	0.10351449978457333	RNA PCR Primer, Index 2 (100% over 36bp)

Adapter Content

Adapter graph

Kmer Content

Kmer graph

Sequence	Count	PValue	Obs/Exp Max	Max Obs/Exp Position
TAGTATG	55	1.8189894E-12	44.013924	43
CTAGTAT	50	2.7284841E-11	44.009556	42
CACGTCA	35	1.4475518E-7	44.000187	27
TTCGCCA	75	0.0	44.000187	27
CATGCGA	300	0.0	43.99998	25
ACGTCAC	35	1.4476063E-7	43.99998	28
GCTATGT	40	8.3236955E-9	43.999775	17
AAAGTGC	375	0.0	43.999775	2
ATTATCT	40	8.3236955E-9	43.999775	37
CCAGTAG	340	0.0	43.999775	17
AATTGCC	60	0.0	43.99977	17
TAGGCTA	65	0.0	43.99977	17
TAGGCGT	30	2.529785E-6	43.99977	17
ACGAGGT	70	0.0	43.99977	2
TAGACGC	85	0.0	43.999565	20
CGTTTCT	20	7.859796E-4	43.999565	20
CGATAAA	105	0.0	43.999565	20
TATAAGC	115	0.0	43.99936	16
ATAGATT	220	0.0	43.999355	16
CGTTAGG	30	2.5299505E-6	43.999355	16

Summary

Basic Statistics

Per base sequence quality

Per tile sequence quality

Per sequence quality scores

Per base sequence content

Per sequence GC content

Per base N content

Sequence Length Distribution

Sequence Duplication Levels

Overrepresented sequences

Adapter Content

Kmer Content