FastQCFastQC Report
Mon 5 Dec 2016
JM105_3_CAGATC_L005_R1_001.fastq

Summary

[OK]Basic Statistics

MeasureValue
FilenameJM105_3_CAGATC_L005_R1_001.fastq
File typeConventional base calls
EncodingSanger / Illumina 1.9
Total Sequences11501269
Sequences flagged as poor quality0
Sequence length50
%GC52

[OK]Per base sequence quality

Per base quality graph

[OK]Per tile sequence quality

Per base quality graph

[OK]Per sequence quality scores

Per Sequence quality graph

[FAIL]Per base sequence content

Per base sequence content

[FAIL]Per sequence GC content

Per sequence GC content graph

[OK]Per base N content

N content graph

[OK]Sequence Length Distribution

Sequence length distribution

[FAIL]Sequence Duplication Levels

Duplication level graph

[FAIL]Overrepresented sequences

SequenceCountPercentagePossible Source
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGC491333442.71992942691802RNA PCR Primer, Index 7 (100% over 50bp)
ATGACCTATGAATTGACAGCCTGGAATTCTCGGGTGCCAAGGAACTCCAG2786982.4231934754330156RNA PCR Primer, Index 1 (100% over 29bp)
ATGACCTATGAATTGACAGCCATGGAATTCTCGGGTGCCAAGGAACTCCA2723992.368425605904879RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTGTGGAATTCTCGGGTGCCAAGGAACTCCA1966301.7096374321824834RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGCTTGGAATTCTCGGGTGCCAAGGAACTCCA1317951.1459170288078646RNA PCR Primer, Index 1 (100% over 28bp)
TTGCGGCCCCGGGTTCCTCCCGGGGCTACGCCTGTCTGAGGGTCGCTTGG1131030.983395832233817No Hit
AAGCTGCCAGCTGAAGAACTGTTGGAATTCTCGGGTGCCAAGGAACTCCA1038230.9027090836672023RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGCTGGAATTCTCGGGTGCCAAGGAACTCC914850.795433964721632RNA PCR Primer, Index 1 (100% over 27bp)
TGAGGTAGTAGGTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA856390.7446047910017581RNA PCR Primer, Index 1 (100% over 28bp)
TGGAGTGTGACAATGGTGTTTTGGAATTCTCGGGTGCCAAGGAACTCCAG835670.7265893876580054RNA PCR Primer, Index 1 (100% over 29bp)
TGGAGTGTGACAATGGTGTTTGTTGGAATTCTCGGGTGCCAAGGAACTCC658230.5723107597952887RNA PCR Primer, Index 1 (100% over 27bp)
GTTCTACAGTCCGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA655350.5698066882880489RNA PCR Primer, Index 7 (100% over 35bp)
CCGTCGAGCAGCATTCCGGGCTTCACATCGGAGGGCTCCAGCCGGCCCCG652980.5677460461102162No Hit
CATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTAT548550.4769473698945742RNA PCR Primer, Index 7 (100% over 48bp)
TATTGCACTTGTCCCGGCCTGTTGGAATTCTCGGGTGCCAAGGAACTCCA506030.43997753639185383RNA PCR Primer, Index 1 (100% over 28bp)
CCTGTCTGAGGGTCGCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC494060.42956998918988853RNA PCR Primer, Index 1 (100% over 33bp)
CTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC462490.40212084423031924RNA PCR Primer, Index 2 (100% over 34bp)
TGTAACAGCAACTCCATGTGGATGGAATTCTCGGGTGCCAAGGAACTCCA442470.38471406937790953RNA PCR Primer, Index 1 (100% over 28bp)
AGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGT435890.3789929615592853RNA PCR Primer, Index 1 (100% over 30bp)
TGAGATGAAGCACTGTAGCTCTGGAATTCTCGGGTGCCAAGGAACTCCAG424120.3687593082119895RNA PCR Primer, Index 1 (100% over 29bp)
AACATTCAACGCTGTCGGTGAGTTGGAATTCTCGGGTGCCAAGGAACTCC412820.3589343054231668RNA PCR Primer, Index 1 (100% over 27bp)
TGAGATGAAGCACTGTAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCA398500.3464835054288357RNA PCR Primer, Index 1 (100% over 28bp)
TCCCTGGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGC389110.33831918895210605No Hit
TCAGTAACTGGAATCTGTCCCTTGGAATTCTCGGGTGCCAAGGAACTCCA386350.33591945375766796RNA PCR Primer, Index 1 (100% over 28bp)
TTCAAGTAATCCAGGATAGGTTTGGAATTCTCGGGTGCCAAGGAACTCCA377530.32825073476674616RNA PCR Primer, Index 1 (100% over 28bp)
ACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA375400.3263987652145168RNA PCR Primer, Index 7 (100% over 35bp)
AACATTCAACGCTGTCGGTGAGTGGAATTCTCGGGTGCCAAGGAACTCCA371150.3227035208027914RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCA366400.3185735417543925No Hit
TAACGGAACCCATAATGCAGCTGTGGAATTCTCGGGTGCCAAGGAACTCC358110.3113656414783447RNA PCR Primer, Index 1 (100% over 27bp)
TAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAG328090.28526417389246356RNA PCR Primer, Index 1 (100% over 29bp)
TCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC295520.25694555965954713RNA PCR Primer, Index 1 (100% over 33bp)
TGAGGTAGTAGTTTGTATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA282000.2451903350838938RNA PCR Primer, Index 1 (100% over 28bp)
ACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG281220.24451214905068303RNA PCR Primer, Index 7 (100% over 36bp)
TGTAAACATCCTACACTCTCAGCTTGGAATTCTCGGGTGCCAAGGAACTC266000.23127882671033956RNA PCR Primer, Index 1 (100% over 26bp)
CAGAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCC264690.23013982196225477RNA PCR Primer, Index 1 (100% over 27bp)
AACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGCT257940.22427090436716157No Hit
TTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA254270.22107995213397755RNA PCR Primer, Index 1 (100% over 32bp)
CACCACGTTCCCGTGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC252910.21989747392222544RNA PCR Primer, Index 2 (100% over 34bp)
TGTAAACATCCTTGACTGGAAGCTTGGAATTCTCGGGTGCCAAGGAACTC245700.2136286004613926RNA PCR Primer, Index 1 (100% over 26bp)
AGAGTTCTACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCA239620.20834222727944196RNA PCR Primer, Index 1 (100% over 28bp)
TAGCTTATCAGACTGGTGTTGGTGGAATTCTCGGGTGCCAAGGAACTCCA228730.19887370689269157RNA PCR Primer, Index 1 (100% over 28bp)
TGAGAACTGAATTCCATAGATGGTGGAATTCTCGGGTGCCAAGGAACTCC225630.19617835214531545RNA PCR Primer, Index 1 (100% over 27bp)
TCAGTAACTGGAATCTGTCCCTGTGGAATTCTCGGGTGCCAAGGAACTCC216710.18842268622705896RNA PCR Primer, Index 1 (100% over 27bp)
TCCCTGTGGTCTAGTGGTTAGGATTCGGCGCTCTGGAATTCTCGGGTGCC215600.18745757533364363No Hit
TAGCAGCACGTAAATATTGGAGTGGAATTCTCGGGTGCCAAGGAACTCCA215460.187335849635375RNA PCR Primer, Index 1 (100% over 28bp)
TACAGTCCGACGATCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA215170.18708370354610435RNA PCR Primer, Index 7 (100% over 35bp)
GTTCTACAGTCCGACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC202740.1762762004783994RNA PCR Primer, Index 2 (100% over 34bp)
GATCCATGATGACATTAAAACATAACGTGACTGTTGGATGAAGCTTGCGG194860.16942478260442392No Hit
TCGCTGCGATCCATTGAAAGTCAGCCCTCGATCCAAGTTTTTGTTGGAAT194700.16928566752068835No Hit
TGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATCATCTCGTATGCC187040.16262553288684925RNA PCR Primer, Index 7 (98% over 50bp)
TGAGGTAGTAGATTGAATAGTTTGGAATTCTCGGGTGCCAAGGAACTCCA180900.15728699154849782RNA PCR Primer, Index 1 (100% over 28bp)
GCATTGGTGGTTCAGTGGTAGAATTCTCGCCTGCCACGCGGGAGGCCCGG180080.15657402674435317No Hit
CAACTCTTAGCGGTGGATCACTCGGCTCGTGCGTCGATGAAGAACGCAGC155520.13521986139094738No Hit
TTTGTTCGTTCGGCTCGCGTTATGGAATTCTCGGGTGCCAAGGAACTCCA155040.13480251613974076RNA PCR Primer, Index 1 (100% over 28bp)
TAACACTGTCTGGTAACGATGTTGGAATTCTCGGGTGCCAAGGAACTCCA154950.1347242639051395RNA PCR Primer, Index 1 (100% over 28bp)
TGGACGTGATGAGCAGGTGTTACCGCCCCAGTCTGATGTTTGGTGACTGA148280.1289249038519141No Hit
TGTAAACATCCTACACTCAGCTTGGAATTCTCGGGTGCCAAGGAACTCCA137510.11956071977796538RNA PCR Primer, Index 1 (100% over 28bp)
ATCCATGATGACATTAAAACATAACGTGACTGTTGGATGAAGCTTGCGGA137350.11942160469422983No Hit
TGTAACAGCAACTCCATGTGGAATGGAATTCTCGGGTGCCAAGGAACTCC136900.11903034352122363RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGATGATCTCGTATGC135680.1179695910077401RNA PCR Primer, Index 7 (98% over 50bp)
TTCAGTGATGTTTGACAAATGTCTGACCTGAACTGCAATGTGGACAGATC134780.11718706866172766No Hit
ATGACCTATGAATTGACAGCCATTGGAATTCTCGGGTGCCAAGGAACTCC133730.11627412592471317RNA PCR Primer, Index 1 (100% over 27bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAAGATCATCTCGTATGC131790.11458735553441972RNA PCR Primer, Index 7 (98% over 50bp)
AGAGATGATGACTTCTGTTACCGCCCCAGTCTGAGAAGTCATGACTGATC130820.113743970339273No Hit
GCATTGTGGTTCAGTGGTAGAATTCTCGCCTTGGAATTCTCGGGTGCCAA127940.11123989883203324No Hit
ACAGTAGTCTGCACATTGGTTTGGAATTCTCGGGTGCCAAGGAACTCCAG127610.11095297397182868RNA PCR Primer, Index 1 (100% over 29bp)
CATTATTACTTTTGGTACGCGTGGAATTCTCGGGTGCCAAGGAACTCCAG125390.10902275218499802RNA PCR Primer, Index 1 (100% over 29bp)
CTCGCTGCGATCCATTGAAAGTCAGCCCTCGATCCAAGTTTTTGTTGGAA123900.10772724296771079No Hit
GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCTTGGAATTCTCGGGTGCC123500.10737945525837193No Hit
TGAGAACTGAATTCCATAGATGTGGAATTCTCGGGTGCCAAGGAACTCCA121600.10572746363901235RNA PCR Primer, Index 1 (100% over 28bp)
TTCACAGTGGTTAAGTTCTGCCTGGAATTCTCGGGTGCCAAGGAACTCCA115930.10079757285913406RNA PCR Primer, Index 1 (100% over 28bp)
TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAACAGATCATCTCGTATGC115320.1002671966023923RNA PCR Primer, Index 7 (98% over 50bp)

[WARN]Adapter Content

Adapter graph

[WARN]Kmer Content

Kmer graph

SequenceCountPValueObs/Exp MaxMax Obs/Exp Position
TTAATGC207.821425E-444.0433461
CGGTCAA302.5238642E-644.0148144
CTCGTAA454.802132E-1044.00772542
CGCGTAT502.7284841E-1144.0077242
TCGCGTA502.7284841E-1144.001641
CTACTCC207.859214E-444.00026324
TGCGAAA408.3236955E-944.00026327
TTGCGAA408.3236955E-944.00026326
CATGCGC254.445194E-544.0002625
ATTCGCC351.4475336E-744.0002626
CTGCGTC254.445194E-544.0002626
GGCATAC850.044.0002627
GTCTTGC351.4475336E-744.0002623
ACTCATC254.445194E-544.0002623
CCAAATA454.802132E-1044.0002627
GTCCGTA254.445422E-543.9998829
TAGGCAA254.445422E-543.9998817
CAAGGCG207.8595505E-443.99987817
TAGGCTA1150.043.99987817
AAGGCGG207.8595505E-443.99987818