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
A23 F20 I0 R1	95	76.5	1681216	93.1%	1565212	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,196,508	C→A	100%	intergenic (+2563/‑1229)	ftsQ → / → USA300HOU_1125	cell division protein FtsQ/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,196,508	0	C	A	100.0%	187.8 / ‑6.5	60	intergenic (+2563/‑1229)	ftsQ/USA300HOU_1125	cell division protein FtsQ/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (23/36); minor base G (0/1); total (23/37)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGAC  >  CP000730/1196371‑1196645

ttttttCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAg                                                                                                                                        <  1:723792/139‑1 (MQ=255)

 aTTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGc                                                                                                                                       >  2:60563/1‑141 (MQ=255)

    ttCGGTACAGTTATTACTACTAAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAAt                                                                                                                                    <  2:840159/141‑1 (MQ=255)

       ggtgacgTTACTAACCCTGAATTACTAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCACCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCa                                                                                                                                 <  2:731084/135‑1 (MQ=255)

       ggTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCa                                                                                                                                 >  1:471245/1‑141 (MQ=255)

        gTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCaa                                                                                                                                >  2:393925/1‑141 (MQ=255)

        gTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCaa                                                                                                                                >  1:389025/1‑141 (MQ=255)

         tACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAAc                                                                                                                               <  1:685687/141‑1 (MQ=255)

            aGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTc                                                                                                                            <  2:685642/141‑1 (MQ=255)

                 ttaATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAACAATGAAACTTATaaaa                                                                                                                       >  2:379736/1‑140 (MQ=255)

                     tCCTTAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGa                                                                                                                   <  1:747907/141‑1 (MQ=255)

                     cccTAAATTAGCAGATGACATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTCGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGa                                                                                                                   <  2:441457/140‑1 (MQ=255)

                        tGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGACTc                                                                                                                >  2:254230/1‑141 (MQ=255)

                            ttACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGCTGAATCATTc                                                                                                            >  2:799410/1‑141 (MQ=255)

                               cAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACt                                                                                                         <  2:462013/141‑1 (MQ=255)

                               cAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACt                                                                                                         >  2:756887/1‑141 (MQ=255)

                               cAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCCTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACt                                                                                                         <  1:474799/141‑1 (MQ=255)

                                 aGATGAGATTGTTGTAGCAGTTATTTCAACTGGGTTTGATGACAAACCAACATGACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTc                                                                                                       >  2:405175/1‑141 (MQ=255)

                                       gaTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtc                                                                                                 >  1:698852/1‑141 (MQ=255)

                                        aTTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCCAATtca                                                                                                >  1:731170/1‑141 (MQ=255)

                                         ttgttgTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcat                                                                                               <  1:518962/141‑1 (MQ=255)

                                         ttgttgTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcat                                                                                               <  1:643658/141‑1 (MQ=255)

                                         ttgttgTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGCAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcat                                                                                               <  2:370073/141‑1 (MQ=255)

                                               tAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATg                                                                                         <  2:143511/141‑1 (MQ=255)

                                                 aCAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTGGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGca                                                                                       >  1:440277/1‑141 (MQ=255)

                                                   aGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGcaca                                                                                     <  1:102042/141‑1 (MQ=255)

                                                    gTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACaa                                                                                    <  1:129207/141‑1 (MQ=255)

                                                     ttATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAg                                                                                   >  1:96741/1‑141 (MQ=255)

                                                       aTTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCa                                                                                 <  2:744211/141‑1 (MQ=255)

                                                        ttGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCaa                                                                                >  2:839789/1‑141 (MQ=255)

                                                           cAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTg                                                                             <  1:81823/141‑1 (MQ=255)

                                                            aacgtgTTTGGATGACAAACCAACATTACATGGTCGTACATCTGGGAGCACTGGATTCGGAACAAGCGTAAATACGTAGAGGAATGCAACGTCGAAAGATTAATCATTCACTTCAAATTCATCAAAGGCACAAGTAACGGa                                                                            <  2:178601/136‑1 (MQ=255)

                                                             aCTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGAt                                                                           >  2:614379/1‑141 (MQ=255)

                                                              gtGGTTTTGATGACAAACCAACAGCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATa                                                                          <  2:800371/140‑1 (MQ=255)

                                                               tGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAg                                                                         <  2:593104/141‑1 (MQ=255)

                                                                    ttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTaa                                                                    <  1:756887/141‑1 (MQ=255)

                                                                    ttGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTaa                                                                    >  2:56473/1‑141 (MQ=255)

                                                                     tgatgaCAAACCCACATCACATGGTCGTCAATCGTGTATCACTGGATTCGGACCAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAg                                                                   <  1:110674/141‑1 (MQ=255)

                                                                     tgatgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAg                                                                   >  1:316882/1‑141 (MQ=255)

                                                                          aCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGaaa                                                              <  2:726182/141‑1 (MQ=255)

                                                                            aaaCCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAATTGAAAGa                                                            >  2:270195/1‑141 (MQ=255)

                                                                               ccAACATAACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATACTGTAAGTGAAAGAaca                                                         <  1:415495/141‑1 (MQ=255)

                                                                                 aaCATCACATGGTCTTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAAcaca                                                       <  1:97956/141‑1 (MQ=255)

                                                                                 aaCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAAcaca                                                       <  2:764922/141‑1 (MQ=255)

                                                                                 aaCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATCAATCAACTGCACAAGCAACTGATAGTGTAAGTGAAAGAAcaca                                                       <  2:764980/141‑1 (MQ=255)

                                                                                  aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCGCTTCCAATTCCTCAAATGCACCAGCAACTGATAGTGTACGTGAAAGAACACAt                                                      >  1:646613/1‑141 (MQ=255)

                                                                                       acaTGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAAc                                                 <  1:336536/141‑1 (MQ=255)

                                                                                            gTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAaag                                            <  1:60563/141‑1 (MQ=255)

                                                                                            gTCGTAAATCGGGTAGCACAGGAATCGGTACAAGCGTAAATAAATATATCTTCTTAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAaag                                            <  1:604967/141‑1 (MQ=255)

                                                                                                      tGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGatat                                  <  2:312131/141‑1 (MQ=255)

                                                                                                       ggTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATAtt                                 <  2:204734/141‑1 (MQ=255)

                                                                                                         tAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                               <  2:96741/141‑1 (MQ=255)

                                                                                                             aCTGGATTCGGAACAAGCGTTAGTACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCCCGAGGAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGc                           <  1:785564/141‑1 (MQ=255)

                                                                                                             aCTGGATTAGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGc                           <  1:38221/141‑1 (MQ=255)

                                                                                                                   ttCGGAACAAGGGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCAtt                     <  2:34781/141‑1 (MQ=255)

                                                                                                                          cAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATa              >  1:436746/1‑141 (MQ=255)

                                                                                                                          cAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATa              >  2:733239/1‑141 (MQ=255)

                                                                                                                             gCGTACATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACCAGCAACTGATAGTGTAAGTGAAAGATCACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATagag           >  1:617297/1‑141 (MQ=255)

                                                                                                                             gCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATagag           >  1:8199/1‑141 (MQ=255)

                                                                                                                                      cTTGTAGCAATGCAACTTCTAAAGATGAAGCATTCACTTCAAATTCAGCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGAc  <  2:406457/141‑1 (MQ=255)

GATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGAC  >  CP000730/1196371‑1196645

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