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 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,454,626	A→T	100%	L48L (CTA→CTT)	lyrA →	Lysostaphin resistance protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,454,626	0	A	T	100.0%	151.9 / NA	44	L48L (CTA→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (23/21); total (23/21)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTA  >  USA300TCH1516_ALE/2454490‑2454749

aCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAc                                                                                                                         >  2:297828/1‑141 (MQ=255)

    tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                     >  2:366210/1‑141 (MQ=255)

       aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                  >  1:309775/1‑141 (MQ=255)

       aaTTACTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTGTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                  >  1:268512/1‑141 (MQ=255)

           tCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgct                                                                                                              <  2:29620/141‑1 (MQ=255)

              tgTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                           <  1:12431/140‑1 (MQ=255)

              ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTCATTGCTGCa                                                                                                           >  1:325204/1‑141 (MQ=255)

              ggTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                           >  1:99539/1‑141 (MQ=255)

                           cAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAACATTAATTGCTGCAATGATTTTTATAc                                                                                              >  2:236743/1‑141 (MQ=255)

                              tGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATCCTCg                                                                                           >  1:324347/1‑141 (MQ=255)

                                gcGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                         <  1:226900/140‑1 (MQ=255)

                                aCGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                         >  2:44471/1‑141 (MQ=255)

                                    ttttCGTCTTCTTTTTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTCTATTTTAAGTTACAGATCTTGCCCCATTAATTGCTGCAATCATTTGTATACTCGTTTTCa                                                                                     <  1:110073/141‑1 (MQ=255)

                                    ttttCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCa                                                                                     <  1:201598/141‑1 (MQ=255)

                                     tttCGCTTTCTTTGTCATTACAATGGCGTTATCCAGCATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCaa                                                                                    <  1:48540/141‑1 (MQ=255)

                                          tcttctTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACCCGTTTTCAAAtata                                                                               <  2:271058/141‑1 (MQ=255)

                                             tcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaaaa                                                                            <  1:31854/141‑1 (MQ=255)

                                             tcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaaaa                                                                            <  1:60007/141‑1 (MQ=255)

                                             tcttTGTCATTACAATGGCCTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATaaaa                                                                            <  1:60197/141‑1 (MQ=255)

                                                   tCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTcc                                                                      <  1:224973/141‑1 (MQ=255)

                                                        aCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACtt                                                                 >  1:1326/1‑141 (MQ=255)

                                                         cAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCAGTTGTATACTCGTTATCAAATATAAAAAGGTCCAACTTg                                                                <  1:253908/141‑1 (MQ=255)

                                                             ggCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTACAACTTGCAgg                                                            >  2:374442/1‑141 (MQ=255)

                                                                 ttATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTa                                                        >  2:79544/1‑141 (MQ=255)

                                                                   ttCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaaa                                                      <  1:243497/140‑1 (MQ=255)

                                                                      cATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAAtt                                                   <  1:206327/141‑1 (MQ=255)

                                                                          aTGCTCAGAGATTTCCCGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                               <  1:184292/141‑1 (MQ=255)

                                                                          aTGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                               >  1:307931/1‑141 (MQ=255)

                                                                              tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                           >  1:33045/1‑141 (MQ=255)

                                                                                   gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTg                                      >  1:303816/1‑141 (MQ=255)

                                                                                    aTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTCTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGa                                     <  1:66034/141‑1 (MQ=255)

                                                                                                  aTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGt                       <  1:48989/141‑1 (MQ=255)

                                                                                                    tGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGCACGTCt                     >  2:147891/1‑141 (MQ=255)

                                                                                                    tGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCt                     <  2:224162/141‑1 (MQ=255)

                                                                                                     ggTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTa                    >  2:48944/1‑141 (MQ=255)

                                                                                                       tgtCGAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCCCTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                  >  1:269950/1‑141 (MQ=255)

                                                                                                       tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTAGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                  >  1:242732/1‑141 (MQ=255)

                                                                                                            aaCACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAg             <  1:318758/141‑1 (MQ=255)

                                                                                                              cacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt           >  2:48425/1‑141 (MQ=255)

                                                                                                               cttttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTCTTCTCGTATTCAAAGATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTTAAAGTAATTGAACGTCTATTGCTAGCtt          <  2:289496/139‑1 (MQ=255)

                                                                                                                ttttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTGTCAATCAGGCTGAAATTACTTGAACGTCTATTGCTATCttt         >  2:363467/2‑141 (MQ=255)

                                                                                                                cTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAATTAATTGAACGTCTATTGCTAGCttt         >  1:109010/1‑141 (MQ=255)

                                                                                                                cTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCttt         <  1:297828/141‑1 (MQ=255)

                                                                                                                       tttGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTa  >  2:36708/1‑141 (MQ=255)

ACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTA  >  USA300TCH1516_ALE/2454490‑2454749

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