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	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	266,981	A→G	P228P (CCA→CCG)	USA300HOU_RS01175 →	Staphylocoagulase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	266,981	0	A	G	100.0%	110.3 / NA	32	P228P (CCA→CCG)	USA300HOU_RS01175	Staphylocoagulase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/20); total (12/20)

AGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCACATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACA  >  USA300TCH1516_ALE/266843‑267122

aGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAAtt                                                                                                                                      <  3:353932/148‑1 (MQ=255)

        aGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGa                                                                                                                              <  3:64711/148‑1 (MQ=255)

         ggAAGTATACGATCTCGTATCTGAAATTGGTACACTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCGTGGAGATACAGACAATCCGCTTAAAATTACAAATGaa                                                                                                                             <  4:308487/148‑1 (MQ=255)

                   gATCTTGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTaaaa                                                                                                                   <  4:332453/148‑1 (MQ=255)

                       tcGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATAAAAATAATAAAAAAGa                                                                                                               <  4:393128/148‑1 (MQ=255)

                            tCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTaaaaaa                                                                                                                 >  1:37234/1‑141 (MQ=255)

                             cTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAg                                                                                                                <  2:8266/141‑1 (MQ=255)

                                             aGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCa                                                                                         >  3:66135/1‑148 (MQ=255)

                                                       tattatGGTGATAAGGATTATGGGGAGCACGCGAAAGAGATACGAGCAAAACTGGACTTAATTCTTGGAGATACAGACAATCGGCATAAAAGTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAAATATtaatg                                                                               >  3:226563/1‑148 (MQ=255)

                                                         ttatGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAattat                                                                                    <  2:37234/141‑1 (MQ=255)

                                                          tatGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGAtt                                                                            <  3:232674/148‑1 (MQ=255)

                                                               tGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCttt                                                                       <  3:344014/148‑1 (MQ=255)

                                                                    aGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGa                                                                  <  3:32733/148‑1 (MQ=255)

                                                                           tGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTaaa                                                           <  3:223142/148‑1 (MQ=255)

                                                                              ggAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTCACCCTTAATGTTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACaa                                                        >  3:11525/1‑148 (MQ=255)

                                                                                 gCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAAt                                                     >  3:157058/1‑148 (MQ=255)

                                                                                  caggcgAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTaaa                                                           <  2:7875/138‑1 (MQ=255)

                                                                                    cgcgAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAAATAAACAAAATAGa                                                  >  4:347385/1‑148 (MQ=255)

                                                                                          agagTTACGAGCAAAACTGGACTGAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGaaa                                            <  4:302741/148‑1 (MQ=255)

                                                                                           gagTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAAAAAAAAAAAAAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAAt                                           <  4:56353/148‑1 (MQ=255)

                                                                                               tACGCGCAAAACTGTACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCtat                                       <  4:15518/148‑1 (MQ=255)

                                                                                                     cAAAACTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGaa                                 >  3:356212/1‑148 (MQ=255)

                                                                                                      aaaaCTGGACTTAATCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCtat                                       <  1:50945/141‑1 (MQ=255)

                                                                                                                  aaTCCTTGGCGTGACAGACAAATCGCATAAAATAACAAATGAACGTATTAAAAAAGAAATGAATGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACAGAAATCTAAAACGAAATATAATCCAaca                    >  4:167269/1‑148 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  3:76367/148‑1 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  3:238916/148‑1 (MQ=255)

                                                                                                                   aTCCTTGGAGATACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTacaa                   <  4:43148/148‑1 (MQ=255)

                                                                                                                           agaTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAAc           <  4:243971/148‑1 (MQ=255)

                                                                                                                           agaTACAGACAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAAc           >  3:230154/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  4:137501/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  3:263254/1‑148 (MQ=255)

                                                                                                                                    cAATCCGCATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACa  >  3:13075/1‑148 (MQ=255)

AGCAACTAAGGAAGTATACGATCTCGTATCTGAAATTGATACATTAGTTGTATCATATTATGGTGATAAGGATTATGGGGAGCACGCGAAAGAGTTACGAGCAAAACTGGACTTAATCCTTGGAGATACAGACAATCCACATAAAATTACAAATGAACGTATTAAAAAAGAAATGATTGATGACTTAAATTCAATTATTGATGATTTCTTTATGGAAACTAAACAAAATAGACCGAAATCTATAACGAAATATAATCCTACAACACATAACTATAAAACA  >  USA300TCH1516_ALE/266843‑267122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A