Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,963,768	C→G	V365L (GTA→CTA)	hemY ←	Protoporphyrinogen oxidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,963,768	0	C	G	100.0%	329.7 / NA	87	V365L (GTA→CTA)	hemY	Protoporphyrinogen oxidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (45/42);  total (45/42)

GTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAC  >  USA300TCH1516_ALE/1963680‑1963854                                                                                         |                                                                                       gTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGAt                                                                                      >  1:976236/1‑91 (MQ=255)  tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATa                                                                                     >  1:827452/1‑91 (MQ=255)   catcatTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATAc                                                                                    >  1:704826/1‑91 (MQ=255)        tttGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACg                                                                               >  1:2103433/1‑91 (MQ=255)         ttGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGa                                                                              >  1:2333676/1‑91 (MQ=255)         ttGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGa                                                                              <  1:652991/91‑1 (MQ=255)             cTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCa                                                                          <  1:2943560/91‑1 (MQ=255)               tAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCaaa                                                                        >  1:1280116/1‑91 (MQ=255)                   tctcTACGTACAAGCGATACTAATTCACTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacct                                                                    <  1:409234/91‑1 (MQ=255)                    ctctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacctt                                                                   >  1:1703962/1‑91 (MQ=255)                      ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                 >  1:2394168/1‑91 (MQ=255)                      ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                 <  1:221192/91‑1 (MQ=255)                      ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                 <  1:220645/91‑1 (MQ=255)                      ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                 <  1:1455299/91‑1 (MQ=255)                      ctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttac                                                                 <  1:1599312/91‑1 (MQ=255)                       tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacc                                                                <  1:1814841/91‑1 (MQ=255)                        aCGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCAGAGTATCACTTGGCTTACCTAGATACGCACGAATCAAAaccttacct                                                               <  1:2952623/91‑1 (MQ=255)                        aCGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                               <  1:1680047/91‑1 (MQ=255)                        aCGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacct                                                               <  1:1699907/91‑1 (MQ=255)                         cGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt                                                              >  1:1130377/1‑91 (MQ=255)                          gTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTc                                                             <  1:2195954/91‑1 (MQ=255)                                tCGATACTAATTCATTATCTGTATGATCAGCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGgtgt                                                       <  1:2965059/91‑1 (MQ=255)                                    tACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTgtagta                                                   >  1:2014835/1‑91 (MQ=255)                                    tACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTgtagta                                                   >  1:2016501/1‑91 (MQ=255)                                      cTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTaaa                                                 <  1:2112694/91‑1 (MQ=255)                                       tAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAAt                                                >  1:2134015/1‑91 (MQ=255)                                         aTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATgg                                              <  1:363407/91‑1 (MQ=255)                                          ttCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGc                                             <  1:2704300/91‑1 (MQ=255)                                          ttCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGc                                             <  1:3499421/91‑1 (MQ=255)                                           tCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGcc                                            <  1:3266565/91‑1 (MQ=255)                                            cATTATCTGTATGATGATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCa                                           >  1:3161760/1‑91 (MQ=255)                                              ttATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTACATGGCGAtt                                         >  1:3329561/1‑91 (MQ=255)                                              ttATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtt                                         >  1:2467466/1‑91 (MQ=255)                                              ttATCTCTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtt                                         >  1:2884161/1‑91 (MQ=255)                                                aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtttt                                       >  1:132193/1‑91 (MQ=255)                                                 tCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAttttt                                      <  1:2111823/91‑1 (MQ=255)                                                  cTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtttttt                                     >  1:893652/1‑91 (MQ=255)                                                   tGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATATGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTc                                    <  1:1528996/91‑1 (MQ=255)                                                   tGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTc                                    <  1:3097213/91‑1 (MQ=255)                                                     tATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGa                                  >  1:136921/1‑91 (MQ=255)                                                     tATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGa                                  >  1:2094532/1‑91 (MQ=255)                                                     tATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGa                                  >  1:2523895/1‑91 (MQ=255)                                                      aTGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGAt                                 >  1:2783951/1‑91 (MQ=255)                                                      aTGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGAt                                 >  1:3556836/1‑91 (MQ=255)                                                      aTGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGAt                                 >  1:885130/1‑91 (MQ=255)                                                          tcatcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTcc                             <  1:56700/91‑1 (MQ=255)                                                          tcatcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTcc                             <  1:2297832/91‑1 (MQ=255)                                                          tcatcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTcc                             <  1:393855/91‑1 (MQ=255)                                                          tcatcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTcc                             <  1:2297371/91‑1 (MQ=255)                                                          tcatcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTcc                             <  1:2297178/91‑1 (MQ=255)                                                            atcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCaa                           <  1:1965245/91‑1 (MQ=255)                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                          <  1:1755802/91‑1 (MQ=255)                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                          <  1:1098718/91‑1 (MQ=255)                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                          <  1:1755717/91‑1 (MQ=255)                                                              caACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGt                         >  1:1301956/1‑91 (MQ=255)                                                               aaCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTa                        <  1:2501504/91‑1 (MQ=255)                                                                 ccACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACa                      <  1:1239008/91‑1 (MQ=255)                                                                 ccACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACa                      <  1:1506782/91‑1 (MQ=255)                                                                 ccACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACa                      >  1:1604923/1‑91 (MQ=255)                                                                   acaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATg                    >  1:2095336/1‑91 (MQ=255)                                                                    caGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGc                   >  1:1459355/1‑91 (MQ=255)                                                                     aGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg                  <  1:3707599/91‑1 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGGATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                 >  1:2108836/1‑91 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTGCATGCgg                 >  1:1845172/1‑91 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                 >  1:1645083/1‑91 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                 >  1:1098996/1‑91 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                 >  1:1098801/1‑91 (MQ=255)                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                 >  1:1858593/1‑91 (MQ=255)                                                                        aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTa               >  1:1061294/1‑91 (MQ=255)                                                                         tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa              >  1:2463292/1‑91 (MQ=255)                                                                         tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa              >  1:1042373/1‑91 (MQ=255)                                                                          cACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAAt             >  1:2111491/1‑91 (MQ=255)                                                                           aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATg            >  1:2897634/1‑91 (MQ=255)                                                                           aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATg            <  1:425574/91‑1 (MQ=255)                                                                              tGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCt         <  1:3047697/91‑1 (MQ=255)                                                                               ggTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTg        <  1:3430941/91‑1 (MQ=255)                                                                                gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCGGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt       >  1:3110216/1‑91 (MQ=255)                                                                                gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAatgtatgt       >  1:2982790/1‑91 (MQ=255)                                                                                gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt       >  1:1330642/1‑91 (MQ=255)                                                                                gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt       <  1:2884360/91‑1 (MQ=255)                                                                                gTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGt       >  1:2983447/1‑91 (MQ=255)                                                                                 tttACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTa      <  1:2973131/91‑1 (MQ=255)                                                                                 tttACCTAGATACGCACGAATCAAAACCTCACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTa      <  1:2972721/91‑1 (MQ=255)                                                                                   tACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATc    >  1:928729/1‑91 (MQ=255)                                                                                    aCCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCa   >  1:2676193/1‑91 (MQ=255)                                                                                    aCCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCa   <  1:3581973/91‑1 (MQ=255)                                                                                     ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAc  <  1:439949/91‑1 (MQ=255)                                                                                         |                                                                                       GTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAC  >  USA300TCH1516_ALE/1963680‑1963854

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