Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,243,494	A→T	12.7%	intergenic (+72/+37)	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	2,243,494	0	A	T	12.7%	239.4 / 24.4	80	intergenic (+72/+37)	USA300HOU_RS11475/pyrG	hypothetical protein/CTP synthase
Reads supporting (aligned to +/- strand):  ref base A (39/30);  new base T (3/7);  total (43/37)
Fisher's exact test for biased strand distribution p-value = 1.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.91e-01

AAGAGACTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCG  >  USA300TCH1516_ALE/2243404‑2243583                                                                                           |                                                                                          aaGAGACTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCaa                                                                                           >  1:301827/1‑91 (MQ=255)   gagaCTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATg                                                                                         >  1:1417911/1‑91 (MQ=255)     gaCTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGtt                                                                                       <  1:1215704/91‑1 (MQ=255)     gaCTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGtt                                                                                       <  1:4071074/91‑1 (MQ=255)      aCTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGttt                                                                                      <  1:1840796/91‑1 (MQ=255)       cTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTa                                                                                     <  1:3291474/91‑1 (MQ=255)        ttAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGttaaa                                                                                    <  1:4018689/91‑4 (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                                                                                >  1:348172/1‑91 (MQ=255)            aaTTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAAt                                                                                >  1:2943997/1‑91 (MQ=255)              ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                              <  1:500711/91‑1 (MQ=38)              ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                              <  1:184366/91‑1 (MQ=38)              ttATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGa                                                                              <  1:2897669/91‑1 (MQ=38)               tataAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCATTGTTAAACATTGaa                                                                             <  1:151551/91‑1 (MQ=38)               tataAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGaa                                                                             <  1:3789137/91‑1 (MQ=255)                 taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                           >  1:811538/1‑91 (MQ=255)                 taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                           >  1:3613498/1‑91 (MQ=255)                 taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                           <  1:226460/91‑1 (MQ=255)                 taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                           >  1:44301/1‑91 (MQ=255)                 taAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAg                                                                           <  1:1226185/91‑1 (MQ=255)                   aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                         <  1:1548511/91‑1 (MQ=255)                   aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                         >  1:2739334/1‑91 (MQ=255)                   aaaGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTa                                                                         >  1:1630751/1‑91 (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                                                                       <  1:1528632/91‑1 (MQ=255)                     aGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTAcc                                                                       >  1:3061500/1‑91 (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                                                      >  1:1736579/1‑91 (MQ=255)                                      cATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatt                                                      >  1:2735474/1‑91 (MQ=255)                                      cATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAatt                                                      >  1:2735397/1‑91 (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                                  >  1:831293/1‑91 (MQ=255)                                                          atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                  >  1:835171/1‑91 (MQ=255)                                                          atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                  >  1:228476/1‑91 (MQ=255)                                                          atatTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATAttt                                  >  1:228450/1‑91 (MQ=255)                                                            atTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTa                                <  1:870684/91‑1 (MQ=255)                                                            atTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTa                                >  1:1496494/1‑91 (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)                                                                                         cAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATc   >  1:547852/1‑91 (MQ=255)                                                                                          aaTGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCg  <  1:204389/91‑1 (MQ=255)                                                                                           |                                                                                          AAGAGACTTAGAATTATAAAAGTCACTATTGTTATTTCATACCTTGTCACTAACATAATATTAAAATTATACGAAAAACCGGTACTTTCAATGTTTAACAATGAAAGTACCGGTTTTATTAGCAAATTTATTTATTTTGTTGATATTTTAATGAAGCTTCAATAAATGATTTAAAAATCG  >  USA300TCH1516_ALE/2243404‑2243583

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: ‑