Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A13 F1 I1 R1	86	24.1	1002126	98.1%	983085	121.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,591,739	A→T	I196N (ATC→AAC)	ugpB ←	sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,591,739	0	A	T	100.0%	52.9 / NA	16	I196N (ATC→AAC)	ugpB	sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (7/9); total (7/9)

CCTCGAGCATGGCGATGTGTTTCACCTGCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGATCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAGTTTCGCGGCATAGTCCGCCAGATCCTGCCAGGTTTTCGGCGGCTGTTCCGGGTCTAATCC  >  NC_000913/3591611‑3591851

cctcGAGCATGGCGATGTGTTTCACCTGCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTg                                                                                                        >  2:85715/1‑139 (MQ=255)

 ctcGAGCATGGCGATGTGTTTCACCTGCTCCGGCTTATTGTACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGc                                                                                                       <  1:315231/139‑1 (MQ=255)

             gATGTGTTTCACCTGCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCg                                                                                           <  1:393592/139‑1 (MQ=255)

                    ttCACCTGCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGc                                                                                    <  1:85715/139‑1 (MQ=255)

                           gCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCAt                                                                             >  2:247733/1‑139 (MQ=255)

                            cTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAg                                                                                                             >  1:293384/1‑106 (MQ=255)

                            cTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAg                                                                                                             <  2:293384/106‑1 (MQ=255)

                                                        tCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCgg                                                                        <  1:5971/115‑1 (MQ=255)

                                                        tCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCgg                                                                        >  2:5971/1‑115 (MQ=255)

                                                          cGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAg                                                              <  1:430049/123‑1 (MQ=255)

                                                          cGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAg                                                              >  2:430049/1‑123 (MQ=255)

                                                           gTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAGTTTCGCGGCATAGTCCg                                             <  2:151333/139‑1 (MQ=255)

                                                                           tgttTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAg                                                              >  1:206828/1‑106 (MQ=255)

                                                                           tgttTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAg                                                              <  2:206828/106‑1 (MQ=255)

                                                                                           cGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAGTTTCGCGGCATAGTCCGCCAGATCCTGCCAGGTTTTCGGCGGCTGTTcc             <  2:115266/139‑1 (MQ=255)

                                                                                                      tCCAGGCGCTAAAGTTTTCCAGTTGGTTCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAGTTTCGCGGCATAGTCCGCCAGATCCTGCCAGGTTTTCGGCGGCTGTTCCGGGTCTAATcc  >  2:113962/1‑139 (MQ=255)

CCTCGAGCATGGCGATGTGTTTCACCTGCTCCGGCTTATTGAACTCCAGCACCGCGTCCGTGCCGTCAAAGCCGTTGTTTTTGCTGGCAAACGGCAGACCGTTCCAGGCGCTAAAGTTTTCCAGTTGGATCCAGCCCTGCCAGCCGCTGGCGTAGCCGCACTTCATGCCGGAGGCTTTCAGTTTCGCGGCATAGTCCGCCAGATCCTGCCAGGTTTTCGGCGGCTGTTCCGGGTCTAATCC  >  NC_000913/3591611‑3591851

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A