Detailed 16S Analysis Report: 4001342, SAAG

PART I. SEQUENCE QUALITY CONTROL

1. Assemble paired reads into contigs

Select details from ./makefasta.log:

Number of reads	192	100%
Number of paired reads	190	99%
Number of unpaired reads	2	1%

Select details from ./files/assemble.log:

Number of contigs, total	96	100%
Number of good contigs	72	75%
Number of bad contigs	24	25%

2. Screen primer sequences

Select details from ./primerscreen.out:

Primer Sequences (see file: /home/kobayash/perl/16s/data/primers.27F1492R.fasta)

ID	Sequence
16S_27F_F1	AGaGTTTGATtaTGGCTCAG
16S_27F_F2	AGaGTTTGATtcTGGCTCAG
16S_27F_F3	AGaGTTTGATcaTGGCTCAG
16S_27F_F4	AGaGTTTGATccTGGCTCAG
16S_27F_F5	AGgGTTTGATtaTGGCTCAG
16S_27F_F6	AGgGTTTGATtcTGGCTCAG
16S_27F_F7	AGgGTTTGATcaTGGCTCAG
16S_27F_F8	AGgGTTTGATccTGGCTCAG
16S_1492r_R1	TACGGcTACCTTGTTACGACTT
16S_1492r_R2	TACGGtTACCTTGTTACGACTT
16S_1492r_R3 BH-JGI	GGtTACCTTGTTACGACTT

Primer screening details

Select details from file:	Label	Count	Percent
./files/project.contig	Total number of contigs checked	72	75%
./trimfile.dat	Forward primer trimmed	0	0%
	Reverse primer trimmed	55	57.3%
./noprimerhits.dat	Primer not trimmed	3	3.1%

3. Mask poor quality sub-sequences

Select details from ./SWReadLength.out:

Mean number contigs	1.3
Mean read length	1448.9
Mean total length	1564.3
Mean trimmed length	1479.3
Mode trimmed length	1494

4. Remove short sequences

Select details from ./trimmed.contigs:

Number of contigs before length-trimming	72	75%
Number of contigs after length-trimming	68	70.8%

5. BLAST to identify non-16S/18S sequences

Select details from ./final.contigs.list:

Number of contigs passed	68	70.8%
Number of contigs failed	0	0%

PART II. CLUSTER SEQUENCES

1. Cartesian BLAST, cluster by %id and bp-cov.

Select details from ./clusters/clusters.out:

Number of contigs clustered	65	67.7%

Number of clusters generated	1
Number of clusters merged	0

Select details from ./clusters/clusterSinglets.save:

Number of singlets	3	3.1%

2. Pick representative sequences for each cluster

Select details from ./clusters/clusterReps.dat:

Cluster	Numb. Contigs	% of sample	Numb. Rep. Seqs.
1	65	67.7	5
2	1	1	1
3	1	1	1
4	1	1	1

PART III. IDENTIFY ORGANISMS PRESENT IN SAMPLE

1. BLAST representative sequences against PROKMSA DB

Select details from ./clusters/prokMSA.parsed.blast.data:

Cluster ID	Representative clone	Classification	BP	%ID
1 (65)	SAAG399	Bacillus coagulans str. IDSp	1480	99.7
	SAAG419	Bacillus coagulans str. IDSp	1477	99.6
	SAAG440	Bacillus coagulans str. IDSp	1477	99.4
	SAAG456	Bacillus coagulans str. IDSp	1477	99.5
	SAAG466	Bacillus coagulans str. IDSp	1477	99.7
2 (1)	SAAG394	Bacillus coagulans str. IDSp	1400	99.7
3 (1)	SAAG397	Bacillus coagulans str. IDSp	1483	98.8
4 (1)	SAAG426	Bacillus coagulans str. IDSp	1367	99.4

Species represented in sample

Organism	% of hits
Bacillus coagulans str. IDSp	100%

Link to brief summary page

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