Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,963,768 C→G 53.7% V365L (GTA→CTA)  hemY ← Protoporphyrinogen oxidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,963,7680CG53.7% 20.7 / 149.1 93V365L (GTA→CTA) hemYProtoporphyrinogen oxidase
Reads supporting (aligned to +/- strand):  ref base C (21/22);  new base G (22/28);  total (43/50)
Fisher's exact test for biased strand distribution p-value = 6.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

TGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACT  >  USA300TCH1516_ALE/1963679‑1963855
                                                                                         |                                                                                       
tGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACa                                                                                        >  1:3090173/1‑91 (MQ=255)
tGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACa                                                                                        <  1:3372323/91‑1 (MQ=255)
tGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACATGGTTTACCTACa                                                                                        >  1:3089785/1‑91 (MQ=255)
  tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATa                                                                                      >  1:81977/1‑91 (MQ=255)
  tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATa                                                                                      >  1:2362728/1‑91 (MQ=255)
  tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATa                                                                                      >  1:2362542/1‑91 (MQ=255)
  tcatcaTTTGACTTAAATCTCTACGTACAATCGATACTAATTCAGTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATa                                                                                      <  1:3297408/91‑1 (MQ=255)
   catcatTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATAc                                                                                     >  1:459818/1‑91 (MQ=255)
    atcatTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACg                                                                                    >  1:3880368/1‑91 (MQ=255)
     tcatTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGc                                                                                   <  1:1645930/91‑1 (MQ=255)
      catTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCa                                                                                  >  1:2824060/1‑91 (MQ=255)
       atTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCAc                                                                                 <  1:2404710/91‑1 (MQ=255)
          tGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGaa                                                                              >  1:1830907/1‑91 (MQ=255)
           gACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACACACGAAt                                                                             >  1:2071942/1‑91 (MQ=255)
            aCTTAAATCTCTACGTACAATCGATACTACTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATc                                                                            <  1:3330483/91‑1 (MQ=255)
            aCTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATc                                                                            <  1:2732484/91‑1 (MQ=255)
              ttAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCaa                                                                          >  1:1584979/1‑91 (MQ=255)
                 aaTCTCTACGTACGATCGATACTAATTCATTATCTGTATGATCGTCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAac                                                                       <  1:4154500/91‑1 (MQ=255)
                 aaTCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAac                                                                       <  1:2681959/91‑1 (MQ=255)
                 aaTCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAac                                                                       <  1:2463998/91‑1 (MQ=255)
                   tctcTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAacct                                                                     <  1:2004904/91‑1 (MQ=255)
                   tctcTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacct                                                                     <  1:801802/91‑1 (MQ=255)
                   tctcTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacct                                                                     <  1:667568/91‑1 (MQ=255)
                   tctcTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacct                                                                     <  1:801749/91‑1 (MQ=255)
                   tctcTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacct                                                                     <  1:393931/91‑1 (MQ=255)
                    ctctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacctt                                                                    >  1:2129733/1‑91 (MQ=255)
                    ctctACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAacctt                                                                    >  1:2129762/1‑91 (MQ=255)
                       tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAaccttacc                                                                 >  1:2810069/1‑91 (MQ=255)
                       tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAaccttacc                                                                 >  1:2810535/1‑91 (MQ=255)
                       tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAaccttacc                                                                 >  1:1345052/1‑91 (MQ=255)
                       tACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAaccttacc                                                                 >  1:2810030/1‑91 (MQ=255)
                        aCGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAaccttacct                                                                <  1:2476257/91‑1 (MQ=255)
                         cGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt                                                               >  1:1636236/1‑91 (MQ=255)
                         cGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAaccttacctt                                                               >  1:2665895/1‑91 (MQ=255)
                           tACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTcc                                                             >  1:122083/1‑91 (MQ=255)
                             cAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCgg                                                           <  1:398751/91‑1 (MQ=255)
                             cAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCgg                                                           <  1:398478/91‑1 (MQ=255)
                              aaTCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGgt                                                          <  1:579987/91‑1 (MQ=255)
                               aTCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGgtg                                                         >  1:3702728/1‑91 (MQ=255)
                                tCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGgtgt                                                        <  1:1985378/91‑1 (MQ=255)
                                 cGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTgta                                                       >  1:3637755/1‑91 (MQ=255)
                                    tACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTgtagta                                                    <  1:2168050/91‑1 (MQ=255)
                                         aTTCGTTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATgg                                               <  1:3460871/91‑1 (MQ=255)
                                         aTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATgg                                               <  1:2126148/91‑1 (MQ=255)
                                         aTTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATgg                                               <  1:122435/91‑1 (MQ=255)
                                          ttCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGc                                              <  1:393635/91‑1 (MQ=255)
                                           tCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGcc                                             <  1:849850/91‑1 (MQ=255)
                                           tCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGcc                                             >  1:3950645/1‑91 (MQ=255)
                                            cATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCa                                            >  1:1714999/1‑91 (MQ=255)
                                              ttATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtt                                          <  1:2410456/91‑1 (MQ=255)
                                                aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtttt                                        >  1:3885643/1‑91 (MQ=255)
                                                aTCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCAtttt                                        >  1:2152945/1‑91 (MQ=255)
                                                   tGTATGATCATCAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTc                                     <  1:136795/91‑1 (MQ=255)
                                                    gTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCg                                    <  1:1688743/91‑1 (MQ=255)
                                                    gTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCg                                    <  1:3195807/91‑1 (MQ=255)
                                                        gATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGt                                <  1:1844772/91‑1 (MQ=255)
                                                         atcatcAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTc                               <  1:428345/91‑1 (MQ=255)
                                                         atcatcAACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTc                               <  1:2524998/91‑1 (MQ=255)
                                                           catcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCa                             <  1:1934467/91‑1 (MQ=255)
                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                           >  1:1329470/1‑91 (MQ=255)
                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                           <  1:1305765/91‑1 (MQ=255)
                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                           <  1:1305750/91‑1 (MQ=255)
                                                             tcaACCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAg                           <  1:2309669/91‑1 (MQ=255)
                                                                aCCACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTAc                        <  1:3008679/91‑1 (MQ=255)
                                                                 ccACAGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACa                       >  1:2446648/1‑91 (MQ=255)
                                                                 ccACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACa                       >  1:2924849/1‑91 (MQ=255)
                                                                   acaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATg                     >  1:2161821/1‑91 (MQ=255)
                                                                   acaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATg                     <  1:2987493/91‑1 (MQ=255)
                                                                   acaGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATg                     <  1:197727/91‑1 (MQ=255)
                                                                    caGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGc                    >  1:3253242/1‑91 (MQ=255)
                                                                    caGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGc                    <  1:574706/91‑1 (MQ=255)
                                                                     aGTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg                   >  1:4044540/1‑91 (MQ=255)
                                                                     aGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCTGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg                   <  1:3600872/91‑1 (MQ=255)
                                                                     aGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCg                   <  1:2834172/91‑1 (MQ=255)
                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  <  1:1058000/91‑1 (MQ=255)
                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  >  1:3963367/1‑91 (MQ=255)
                                                                      gTATCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  >  1:2254741/1‑91 (MQ=255)
                                                                      gTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  <  1:1682715/91‑1 (MQ=255)
                                                                      gTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  <  1:3283340/91‑1 (MQ=255)
                                                                      gTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCgg                  >  1:1397449/1‑91 (MQ=255)
                                                                       tATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGt                 <  1:1881002/91‑1 (MQ=255)
                                                                        aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTa                >  1:3790196/1‑91 (MQ=255)
                                                                        aTCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTa                >  1:546461/1‑91 (MQ=255)
                                                                         tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa               >  1:3244443/1‑91 (MQ=255)
                                                                         tCACCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa               >  1:3244676/1‑91 (MQ=255)
                                                                         tCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTaa               <  1:3035486/91‑1 (MQ=255)
                                                                           aCCTGGTTTACCTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATg             >  1:3824718/1‑91 (MQ=255)
                                                                              tGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCt          <  1:1053470/91‑1 (MQ=255)
                                                                                     ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAc   <  1:4006237/91‑1 (MQ=255)
                                                                                     ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAc   <  1:2321146/91‑1 (MQ=255)
                                                                                     ccTAGATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAc   >  1:1021430/1‑91 (MQ=255)
                                                                                     ccTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCAc   >  1:2212822/1‑91 (MQ=255)
                                                                                      cTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACt  >  1:823035/1‑91 (MQ=255)
                                                                                         |                                                                                       
TGTCATCATTTGACTTAAATCTCTACGTACAATCGATACTAATTCATTATCTGTATGATCATCAACCACAGTATCACCTGGTTTACCTACATACGCACGAATCAAAACCTTACCTTCCGGTGTAGTAAATGGCCATTTTTTCGATGTCCAAGTACATGCGGTAATGTCTGTATCACT  >  USA300TCH1516_ALE/1963679‑1963855

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑