Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,243,499	T→A	19.3%	intergenic (+77/+32)	USA300HOU_RS11475 → / ← pyrG	hypothetical protein/CTP synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,243,499	0	T	A	19.3%	211.9 / 43.4	83	intergenic (+77/+32)	USA300HOU_RS11475/pyrG	hypothetical protein/CTP synthase
Reads supporting (aligned to +/- strand):  ref base T (39/28);  new base A (10/6);  total (49/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCGGGTGCG  >  USA300TCH1516_ALE/2243409‑2243589                                                                                           |                                                                                           aCTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGttt                                                                                            <  1:1840796/91‑1 (MQ=255)  cTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTa                                                                                           <  1:3291474/91‑1 (MQ=255)    tAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAAc                                                                                         <  1:3989151/91‑1 (MQ=255)     aGAATTATAAAAGTCACTATTGTTATTTAATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACa                                                                                        >  1:1284876/1‑91 (MQ=255)       aaTTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACatt                                                                                      <  1:2856633/91‑3 (MQ=38)       aaTTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAGTGTTTAACAAt                                                                                      >  1:3761955/1‑91 (MQ=255)       aaTTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAAt                                                                                      >  1:2943997/1‑91 (MQ=255)       aaTTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAAt                                                                                      >  1:348172/1‑91 (MQ=255)         ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                                    <  1:2897669/91‑1 (MQ=38)         ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                                    <  1:500711/91‑1 (MQ=38)         ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                                    <  1:184366/91‑1 (MQ=38)          tataAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGaa                                                                                   <  1:151551/91‑1 (MQ=38)          tataAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGaa                                                                                   <  1:3789137/91‑1 (MQ=255)            taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                                 >  1:3613498/1‑91 (MQ=255)            taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                                 >  1:811538/1‑91 (MQ=255)            taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                                 >  1:44301/1‑91 (MQ=255)            taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                                 <  1:226460/91‑1 (MQ=255)            taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                                 <  1:1226185/91‑1 (MQ=255)              aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                               >  1:1630751/1‑91 (MQ=255)              aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                               >  1:2739334/1‑91 (MQ=255)              aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                               <  1:1548511/91‑1 (MQ=255)               aaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAc                                                                              <  1:983229/91‑1 (MQ=255)               aaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAc                                                                              <  1:3814542/91‑1 (MQ=255)                aGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAcc                                                                             >  1:3448480/1‑91 (MQ=255)                aGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAcc                                                                             <  1:1528631/91‑1 (MQ=255)                aGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAcc                                                                             >  1:3061500/1‑91 (MQ=255)                aGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAcc                                                                             <  1:1528632/91‑1 (MQ=255)                  tCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCgg                                                                           <  1:1955528/91‑1 (MQ=255)                   cACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGt                                                                          <  1:2360968/91‑1 (MQ=255)                   cACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGt                                                                          >  1:736703/1‑91 (MQ=255)                      tATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGtttt                                                                       <  1:3630509/91‑1 (MQ=255)                       aTTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGAAAGTACCGGttttt                                                                      <  1:3113607/91‑2 (MQ=25)                         tGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTttatt                                                                    >  1:3661448/1‑91 (MQ=255)                          gTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTttatta                                                                   <  1:1814608/91‑1 (MQ=255)                               ttCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACTGGTTTTATTAGCaaa                                                              >  1:312981/1‑91 (MQ=255)                               ttCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCaaa                                                              >  1:3902698/1‑91 (MQ=255)                                 cATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatt                                                            >  1:2735474/1‑91 (MQ=255)                                 cATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatt                                                            >  1:2735397/1‑91 (MQ=255)                                 cATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatt                                                            >  1:1736579/1‑91 (MQ=255)                                   tACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAattta                                                          <  1:934282/91‑1 (MQ=255)                                    aCCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatttat                                                         >  1:1720561/1‑91 (MQ=255)                                    aCCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatttat                                                         <  1:718368/91‑1 (MQ=255)                                     ccTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatttatt                                                        <  1:2781942/91‑1 (MQ=255)                                      cTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatttattt                                                       >  1:722527/1‑91 (MQ=255)                                           cACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTAtttt                                                  >  1:2908429/1‑91 (MQ=255)                                               aaCATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTCCCGGTTTTATTAGCAAGTTTATTTATTatgttg                                              >  1:14198/1‑91 (MQ=255)                                               aaCATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTttgttg                                              <  1:526818/91‑1 (MQ=255)                                                aCATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGa                                             <  1:1690468/91‑1 (MQ=255)                                                     atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                        >  1:228476/1‑91 (MQ=255)                                                     atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                        >  1:228450/1‑91 (MQ=255)                                                     atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                        >  1:835171/1‑91 (MQ=255)                                                     atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                        >  1:831293/1‑91 (MQ=255)                                                       atTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTa                                      >  1:1496494/1‑91 (MQ=255)                                                       atTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTa                                      <  1:870684/91‑1 (MQ=255)                                                        ttAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTaa                                     >  1:820703/1‑91 (MQ=255)                                                           aaaTTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGa                                  >  1:522770/1‑91 (MQ=255)                                                             aTTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAg                                >  1:3653789/1‑91 (MQ=255)                                                              ttATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGc                               <  1:3574311/91‑1 (MQ=255)                                                                ataCGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCtt                             >  1:235884/1‑91 (MQ=255)                                                                ataCGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCtt                             >  1:1140009/1‑91 (MQ=255)                                                                 taCGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTc                            >  1:3506486/1‑91 (MQ=255)                                                                 taCGAAAAACCGGTACTTTCAATGTTTAACAATGAAACTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTc                            >  1:3506427/1‑91 (MQ=255)                                                                  aCGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCa                           <  1:1077682/91‑1 (MQ=255)                                                                   cGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCaa                          <  1:1121537/91‑1 (MQ=255)                                                                   cGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCaa                          <  1:2436843/91‑1 (MQ=255)                                                                     aaaaaGCGGTACTTTCAATGTTTAATAATGAAAGTACCGGTTTTATTAGCAAAGTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATa                        <  1:3856271/91‑1 (MQ=39)                                                                           cGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGAt                  <  1:3117377/91‑1 (MQ=255)                                                                            ggTACTTTCATTGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATGTATTTATTGTGTTGATATTTTAATGAAGCTTCAATAAATGAtt                 >  1:2698173/1‑91 (MQ=25)                                                                             gTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGAttt                >  1:3896066/1‑91 (MQ=255)                                                                             gTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGAttt                >  1:3344471/1‑91 (MQ=255)                                                                              tACTTTCATTGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTa               >  1:3249831/1‑91 (MQ=37)                                                                              tACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTa               >  1:595878/1‑91 (MQ=255)                                                                                cTTTCATTGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTaaa             >  1:3060/1‑91 (MQ=37)                                                                                cTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTaaa             >  1:3298384/1‑91 (MQ=255)                                                                                   tCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAAt          <  1:547184/91‑1 (MQ=255)                                                                                    cattGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATc         >  1:783035/4‑91 (MQ=38)                                                                                    cattGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATc         >  1:2776732/4‑91 (MQ=38)                                                                                    cattGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATc         >  1:24072/4‑91 (MQ=38)                                                                                    cAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATc         >  1:547852/1‑91 (MQ=255)                                                                                     attGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCg        >  1:3910292/3‑91 (MQ=38)                                                                                     attGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCg        >  1:1957871/3‑91 (MQ=38)                                                                                     attGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCg        >  1:1753096/3‑91 (MQ=38)                                                                                     aaTGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCg        <  1:204389/91‑1 (MQ=255)                                                                                      ttGTTAAACATTGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCgg       >  1:757395/2‑91 (MQ=255)                                                                                         tttAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCGGGTg    >  1:999383/1‑91 (MQ=255)                                                                                           tAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCGGGTGCg  <  1:3373103/91‑1 (MQ=255)                                                                                           |                                                                                           ACTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCGGGTGCG  >  USA300TCH1516_ALE/2243409‑2243589

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: ‑