FastQC Analysis of 2016-09-28 MiSeq data (14 pairs of samples)

Click on link to see the HTML-formatted FastQC output:

Mycobacterium abscessus316292K_S9_L001_R1_001_fastqc.html316292K_S9_L001_R2_001_fastqc.html
Mycobacterium abscessus327999Y_S10_L001_R1_001_fastqc.html327999Y_S10_L001_R2_001_fastqc.html
Mycobacterium abscessus328777F_S11_L001_R1_001_fastqc.html328777F_S11_L001_R2_001_fastqc.html
Mycobacterium abscessus332334Q_S12_L001_R1_001_fastqc.html332334Q_S12_L001_R2_001_fastqc.html
Mycobacterium abscessus335202Y_S8_L001_R1_001_fastqc.html335202Y_S8_L001_R2_001_fastqc.html
Mycobacterium abscessus336256D_S13_L001_R1_001_fastqc.html336256D_S13_L001_R2_001_fastqc.html
Mycobacterium abscessus403922K_S7_L001_R1_001_fastqc.html403922K_S7_L001_R2_001_fastqc.html
Klebsiella pneumoniaeBB429684_S6_L001_R1_001_fastqc.htmlBB429684_S6_L001_R2_001_fastqc.html
Klebsiella pneumoniaeBR679314_S2_L001_R1_001_fastqc.htmlBR679314_S2_L001_R2_001_fastqc.html
Klebsiella pneumoniaeBS546872_S3_L001_R1_001_fastqc.htmlBS546872_S3_L001_R2_001_fastqc.html
Klebsiella pneumoniaeBS546899_S4_L001_R1_001_fastqc.htmlBS546899_S4_L001_R2_001_fastqc.html
Klebsiella pneumoniaeBS546900_S5_L001_R1_001_fastqc.htmlBS546900_S5_L001_R2_001_fastqc.html
Escherichia coli ESBBI120654_S1_L001_R1_001_fastqc.htmlBI120654_S1_L001_R2_001_fastqc.html
n/aUndetermined_S0_L001_R1_001_fastqc.htmlUndetermined_S0_L001_R2_001_fastqc.html

Reads trimmed to "standard" quality values resulting in following reduction in short-reads and called bases

Untrimmed and trimmed FASTQ read and base quantities grouped in pairs (2x untrimmed then 2x trimmed).

Readset NameTotal seqsTotalbases
316292K_S9_L001_R1_001742,584177,128,955
316292K_S9_L001_R2_001742,584177,162,788
316292K_trimmoed/316292K_forward_paired674,343129,533,906
316292K_trimmoed/316292K_reverse_paired674,343144,801,831

Readset NameTotal seqsTotalbases
327999Y_S10_L001_R1_0011,875,856440,601,759
327999Y_S10_L001_R2_0011,875,856441,638,645
327999Y_trimmoed/327999Y_forward_paired1,591,477349,088,122
327999Y_trimmoed/327999Y_reverse_paired1,591,477279,330,670

Readset NameTotal seqsTotalbases
328777F_S11_L001_R1_0011,699,450399,645,887
328777F_S11_L001_R2_0011,699,450400,233,175
328777F_trimmoed/328777F_forward_paired1,516,093330,421,432
328777F_trimmoed/328777F_reverse_paired1,516,093284,707,580

Readset NameTotal seqsTotalbases
332334Q_S12_L001_R1_0011,140,291271,030,092
332334Q_S12_L001_R2_0011,140,291271,213,173
332334Q_trimmoed/332334Q_forward_paired994,356218,318,293
332334Q_trimmoed/332334Q_reverse_paired994,356181,004,804

Readset NameTotal seqsTotalbases
335202Y_S8_L001_R1_0011,600,981377,621,310
335202Y_S8_L001_R2_0011,600,981377,671,472
335202Y_trimmoed/335202Y_forward_paired1,557,189354,247,767
335202Y_trimmoed/335202Y_reverse_paired1,557,189343,700,733

Readset NameTotal seqsTotalbases
336256D_S13_L001_R1_0011,373,404324,961,996
336256D_S13_L001_R2_0011,373,404325,282,735
336256D_trimmoed/336256D_forward_paired1,199,056261,543,131
336256D_trimmoed/336256D_reverse_paired1,199,056217,668,275

Readset NameTotal seqsTotalbases
403922K_S7_L001_R1_0011,762,842416,425,749
403922K_S7_L001_R2_0011,762,842416,823,644
403922K_trimmoed/403922K_forward_paired1,604,003350,015,217
403922K_trimmoed/403922K_reverse_paired1,604,003306,400,599

Readset NameTotal seqsTotalbases
BB429684_S6_L001_R1_0011,060,233252,364,523
BB429684_S6_L001_R2_0011,060,233252,420,598
BB429684_trimmoed/BB429684_forward_paired1,001,932220,870,383
BB429684_trimmoed/BB429684_reverse_paired1,001,932204,707,463

Readset NameTotal seqsTotalbases
BI120654_S1_L001_R1_0011,277,593302,436,969
BI120654_S1_L001_R2_0011,277,593302,517,080
BI120654_trimmoed/BI120654_forward_paired1,208,647271,889,210
BI120654_trimmoed/BI120654_reverse_paired1,208,647247,107,444

Readset NameTotal seqsTotalbases
BR679314_S2_L001_R1_0011,144,339272,443,147
BR679314_S2_L001_R2_0011,144,339272,520,405
BR679314_trimmoed/BR679314_forward_paired1,053,552234,982,621
BR679314_trimmoed/BR679314_reverse_paired1,053,552205,712,344

Readset NameTotal seqsTotalbases
BS546872_S3_L001_R1_0011,322,144314,358,018
BS546872_S3_L001_R2_0011,322,144314,486,829
BS546872_trimmoed/BS546872_forward_paired1,222,929272,226,210
BS546872_trimmoed/BS546872_reverse_paired1,222,929240,494,098

Readset NameTotal seqsTotalbases
BS546899_S4_L001_R1_0011,198,447285,282,076
BS546899_S4_L001_R2_0011,198,447285,338,671
BS546899_trimmoed/BS546899_forward_paired1,133,010249,914,568
BS546899_trimmoed/BS546899_reverse_paired1,133,010231,804,316

Readset NameTotal seqsTotalbases
BS546900_S5_L001_R1_0011,152,195274,282,556
BS546900_S5_L001_R2_0011,152,195274,334,680
BS546900_trimmoed/BS546900_forward_paired1,091,998241,650,145
BS546900_trimmoed/BS546900_reverse_paired1,091,998224,298,524

Readset NameTotal seqsTotalbases
Undetermined_S0_L001_R1_001702,761167,859,405
Undetermined_S0_L001_R2_001702,761168,071,452
Undetermined_trimmoed/Undetermined_forward_paired500,852109,881,945
Undetermined_trimmoed/Undetermined_reverse_paired500,85297,076,564