Copa del RACE


Side-by-side comparison of 454 sequencing results from CRG vs. Sevilla
Sample: 5T (5'RACE on Testis)

I - Basic FastQC read stats

Barcelona


 		Sevilla

[FAIL] Basic Statistics

Measure Value
Filename 5T.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 208049
Sequence length 40-829
%GC 45

[FAIL] Per base sequence quality

Per base quality graph

[FAIL] Per sequence quality scores

Per Sequence quality graph

[FAIL] Per base sequence content

Per base sequence content

[FAIL] Per base GC content

Per base GC content graph

[FAIL] Per sequence GC content

Per sequence GC content graph

[FAIL] Per base N content

N content graph

[FAIL] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[FAIL] Overrepresented sequences

Sequence Count Percentage Possible Source
CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGTACGCG 42476 20.416344226600465 No Hit
CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGTTACTT 1244 0.5979360631389721 No Hit

[FAIL] Basic Statistics

Measure Value
Filename 5T.fastq
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 845357
Sequence length 40-1596
%GC 43

[FAIL] Per base sequence quality

Per base quality graph

[FAIL] Per sequence quality scores

Per Sequence quality graph

[FAIL] Per base sequence content

Per base sequence content

[FAIL] Per base GC content

Per base GC content graph

[FAIL] Per sequence GC content

Per sequence GC content graph

[FAIL] Per base N content

N content graph

[FAIL] Sequence Length Distribution

Sequence length distribution

[FAIL] Sequence Duplication Levels

Duplication level graph

[FAIL] Overrepresented sequences

Sequence Count Percentage Possible Source
CTAATACGACTCACTATAGGGCAAGCAGTGGTATCAACGCAGAGTACGCG 237291 28.06991602364445 No Hit
CTAATACGACTCACTATAGGGCTGTGACTAGTATGTTGAGTCCTGTAAGT 11071 1.3096242179339617 No Hit


II - Newbler assembly stats


Barcelona

 Sevilla
208049 total reads.
189211 (91%) input to Newbler v2.5p1-internal-10Jun23-1.

        numAlignedReads    = 111377, 58.86%;
        numAlignedBases    = 33876333, 57.30%;
        inferredReadError = 1.57%, 532790;

        numberAssembled = 88957; (47%)
        numberPartial   = 22297;
        numberSingleton = 73790; (39%)
        numberRepeat    = 186;
        numberOutlier   = 3554;
        numberTooShort  = 427;
        numberOfIsotigs       = 4423;
        avgContigCnt          = 2.0;
        largestContigCnt      = 16;
        numberWithOneContig   = 2812;

        numberOfBases     = 2586937;
        avgIsotigSize     = 584;
        N50IsotigSize     = 587;
        largestIsotigSize = 3141;

 845357 total reads.
835080 (99%) input to Newbler v2.6.

        numAlignedReads    = 589924, 70.64%;
        numAlignedBases    = 300516134, 69.44%;
        inferredReadError = 0.91%, 2744346;

        numberAssembled = 504405; (60%)
        numberPartial   = 85416;
        numberSingleton = 214098; (26%)
        numberRepeat    = 444;
        numberOutlier   = 22477;
        numberTooShort  = 8240;
        numberOfIsotigs       = 17939;
        avgContigCnt          = 1.9;
        largestContigCnt      = 14;
        numberWithOneContig   = 10968;

        numberOfBases     = 22496014;
        avgIsotigSize     = 1254;
        N50IsotigSize     = 1328;
        largestIsotigSize = 8287;

III - BLAT genome mapping stats (raw reads)


Barcelona

 		Sevilla

185847 reads mapped to hg19 (89%).


Genomic distribution of aligned reads

5T.barplot_crg.ps.png
Fraction of reads aligned inside targeted regions vs. min % sequence identity threshold

5T.fractionMappedToTarget_barplot_crg.ps.png
826262 reads mapped to hg19 (98%).


Genomic distribution of aligned reads

5T.barplot_sevilla.ps.png

Fraction of reads aligned inside targeted regions vs. min % sequence identity threshold

5T.fractionMappedToTarget_barplot_sevilla.ps.png