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
A1 F169 I1 R1	59	38.6	831760	90.8%	755238	148.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	266,981	A→G	P228P (CCA→CCG)	USA300HOU_0238 →	staphylocoagulase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	266,981	0	A	G	100.0%	90.1 / NA	27	P228P (CCA→CCG)	USA300HOU_0238	staphylocoagulase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (11/16); total (11/16)

AGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCACATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACA  >  CP000730/266843‑267122

aGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAAtt                                                                                                                                      <  1:353932/148‑1 (MQ=255)

        aGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGa                                                                                                                              <  1:64711/148‑1 (MQ=255)

         ggAAGTATACGATCTCGTATCTGAAATTGGTACACTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCGTGGAGATACAGACAATCCGCTTAAAATTACAAATGaa                                                                                                                             <  2:308487/148‑1 (MQ=255)

                   gATCTTGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTaaaa                                                                                                                   <  2:332453/148‑1 (MQ=255)

                       tcGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATAAAAATAATAAAAAAGa                                                                                                               <  2:393128/148‑1 (MQ=255)

                                             aGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCa                                                                                         >  1:66135/1‑148 (MQ=255)

                                                       tattatGGTGATAAGGATTATGGGGAGCACGCGAAAGAGATACGAGCAAAACTGGACTTAATTCTTGGAGATACAGACAATCGGCATAAAAGTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAAATATtaatg                                                                               >  1:226563/1‑148 (MQ=255)

                                                          tatGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGAtt                                                                            <  1:232674/148‑1 (MQ=255)

                                                               tGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCttt                                                                       <  1:344014/148‑1 (MQ=255)

                                                                    aGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGa                                                                  <  1:32733/148‑1 (MQ=255)

                                                                           tGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTaaa                                                           <  1:223142/148‑1 (MQ=255)

                                                                              ggAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTCACCCTTAATGTTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACaa                                                        >  1:11525/1‑148 (MQ=255)

                                                                                 gCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAAt                                                     >  1:157058/1‑148 (MQ=255)

                                                                                    cgcgAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAAATAAACAAAATAGa                                                  >  2:347385/1‑148 (MQ=255)

                                                                                          agagTTACGAGCAAAACTGGACTGAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGaaa                                            <  2:302741/148‑1 (MQ=255)

                                                                                           gagTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAAAAAAAAAAAAAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAAt                                           <  2:56353/148‑1 (MQ=255)

                                                                                               tACGCGCAAAACTGTACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCtat                                       <  2:15518/148‑1 (MQ=255)

                                                                                                     cAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGaa                                 >  1:356212/1‑148 (MQ=255)

                                                                                                                  aaTCCTTGGCGTGACAGACAAATCGCATAAAATAACAAATGAACGTATTAAAAAAGAAATGAATGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACAGAAATCTAAAACGAAATATAATCCAaca                    >  2:167269/1‑148 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  1:238916/148‑1 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  1:76367/148‑1 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  2:43148/148‑1 (MQ=255)

                                                                                                                           agaTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAAc           <  2:243971/148‑1 (MQ=255)

                                                                                                                           agaTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAAc           >  1:230154/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  2:137501/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  1:13075/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  1:263254/1‑148 (MQ=255)

AGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCACATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACA  >  CP000730/266843‑267122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A