Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	410,464	A→T	6.9%	I522I (ATT→ATA)	yitJ ←	Bifunctional homocysteine S‑methyltransferase/5,10‑methylenetetrahydrofolate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	410,464	0	A	T	6.9%	298.6 / 10.6	87	I522I (ATT→ATA)	yitJ	Bifunctional homocysteine S‑methyltransferase/5,10‑methylenetetrahydrofolate reductase
Reads supporting (aligned to +/- strand):  ref base A (44/37);  new base T (3/3);  total (47/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.85e-01

TTCAAATTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTGTGTTA  >  USA300TCH1516_ALE/410374‑410549                                                                                           |                                                                                      ttCAAATTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATa                                                                                       >  1:3528149/1‑91 (MQ=255)    aaaTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATg                                                                                    <  1:1808539/91‑1 (MQ=255)     aaTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATTATGc                                                                                   <  1:1388302/91‑1 (MQ=255)      aTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATTATGcc                                                                                  <  1:440381/91‑1 (MQ=255)      aTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGcc                                                                                  <  1:758631/91‑1 (MQ=255)      aTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGcc                                                                                  <  1:3248272/91‑1 (MQ=255)      aTTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGcc                                                                                  <  1:1766194/91‑1 (MQ=255)       ttgttgTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCt                                                                                 <  1:1262307/91‑1 (MQ=255)       ttgttgTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCt                                                                                 >  1:171280/1‑91 (MQ=255)        tgttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTa                                                                                >  1:2479081/1‑91 (MQ=255)        tgttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTa                                                                                >  1:2478892/1‑91 (MQ=255)         gttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTAt                                                                               >  1:2716522/1‑91 (MQ=255)         gttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTAt                                                                               >  1:1453133/1‑91 (MQ=255)          ttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATg                                                                              <  1:4070605/91‑1 (MQ=255)          ttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATg                                                                              >  1:2789647/1‑91 (MQ=255)          ttgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATg                                                                              >  1:2789839/1‑91 (MQ=255)           tgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATTATGCCTAtcg                                                                             <  1:2541206/91‑3 (MQ=255)           tgtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGa                                                                             >  1:3985514/1‑91 (MQ=255)            gtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaa                                                                            <  1:705859/91‑1 (MQ=255)            gtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaa                                                                            <  1:3052707/91‑1 (MQ=255)            gtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaa                                                                            >  1:3187070/1‑91 (MQ=255)            gtAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaa                                                                            >  1:3600577/1‑91 (MQ=255)             tAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaaa                                                                           >  1:1729259/1‑91 (MQ=255)              aaaaTTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGaaaa                                                                          <  1:562183/91‑1 (MQ=255)                aaTTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAAt                                                                        <  1:877673/91‑1 (MQ=255)                 aTTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATg                                                                       <  1:1901028/91‑1 (MQ=255)                    tCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGtt                                                                    >  1:3335787/1‑91 (MQ=255)                    tCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGtt                                                                    <  1:970984/91‑1 (MQ=255)                      aTCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAGATGGTTTg                                                                  >  1:550152/1‑91 (MQ=255)                      aTCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTg                                                                  >  1:2037625/1‑91 (MQ=255)                        cTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGtt                                                                >  1:3666882/1‑91 (MQ=255)                           aCATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCaa                                                             >  1:1144353/1‑91 (MQ=255)                           aCATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCaa                                                             <  1:1450828/91‑1 (MQ=255)                           aCATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCaa                                                             <  1:1659602/91‑1 (MQ=255)                            cATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAg                                                            >  1:2948589/1‑91 (MQ=255)                                  gATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTa                                                      >  1:4110499/1‑91 (MQ=255)                                  gATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTa                                                      >  1:4110392/1‑91 (MQ=255)                                   aTTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAg                                                     >  1:2572651/1‑91 (MQ=255)                                   aTTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAg                                                     >  1:930668/1‑91 (MQ=255)                                    ttCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGt                                                    >  1:506650/1‑91 (MQ=255)                                        tGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCa                                                >  1:3050650/1‑91 (MQ=255)                                         ggCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCAt                                               >  1:2810802/1‑91 (MQ=255)                                         ggCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCAt                                               >  1:2813929/1‑91 (MQ=255)                                         ggCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCAt                                               >  1:1826882/1‑91 (MQ=255)                                         ggCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCAt                                               >  1:1828598/1‑91 (MQ=255)                                          gCACTTCATTATGCAAAAAGAGTGCATTTTTGTAACTTGTGATAGGCATAATGGCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATg                                              <  1:3865525/91‑1 (MQ=255)                                           cACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATgg                                             <  1:446484/91‑1 (MQ=255)                                           cACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATgg                                             <  1:1968210/91‑1 (MQ=255)                                             cTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTa                                           >  1:1593166/1‑91 (MQ=255)                                             cTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTa                                           >  1:2184192/1‑91 (MQ=255)                                                cATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAAt                                        >  1:2410489/1‑91 (MQ=255)                                                cATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAAt                                        >  1:2579842/1‑91 (MQ=255)                                                cATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAAt                                        >  1:2410462/1‑91 (MQ=255)                                                cATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAAt                                        >  1:3488309/1‑91 (MQ=255)                                                 aTTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAAtt                                       >  1:3465099/1‑91 (MQ=255)                                                   tATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTc                                     >  1:2066047/1‑91 (MQ=255)                                                     tGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCaa                                   <  1:2877758/91‑1 (MQ=255)                                                       cAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATg                                 <  1:360581/91‑1 (MQ=255)                                                        aaaaaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGa                                <  1:1250028/91‑1 (MQ=255)                                                         aaaaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTGTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGAt                               <  1:3503380/91‑1 (MQ=255)                                                          aaaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGAtt                              <  1:1699196/91‑1 (MQ=255)                                                          aaaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGAtt                              <  1:1699043/91‑1 (MQ=255)                                                          aaaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGAtt                              <  1:2625756/91‑1 (MQ=255)                                                           aaGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGAttt                             <  1:44792/91‑1 (MQ=255)                                                                tGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTctct                        >  1:2974426/1‑91 (MQ=255)                                                                 gCGTTTTTGTAACTTGCGATAGGCATAATGCCTCTGACAAATGGTTCGTTCAAGTGCTTCGTGGCATGGTAAATTTCAATGATTTTCTCtt                       >  1:3312256/1‑91 (MQ=255)                                                                 gCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCtt                       >  1:3802335/1‑91 (MQ=255)                                                                 gCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCtt                       >  1:3127614/1‑91 (MQ=255)                                                                  cGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCttt                      <  1:2814507/91‑1 (MQ=255)                                                                    tttttGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGc                    <  1:2294135/91‑1 (MQ=255)                                                                    tttttGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGc                    <  1:3012464/91‑1 (MQ=255)                                                                      tttGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTg                  >  1:3929336/1‑91 (MQ=255)                                                                      tttGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTg                  >  1:3929597/1‑91 (MQ=255)                                                                        tGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTa                <  1:1653414/91‑1 (MQ=255)                                                                          gtaCTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTATCTTTGCTGTaca              >  1:4145198/3‑91 (MQ=255)                                                                           aaCTTGCGATAGGCATAATTCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTacac             <  1:3111702/91‑1 (MQ=255)                                                                            aCTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGGTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACg            >  1:3492088/1‑91 (MQ=255)                                                                             cTTACGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACgg           <  1:3218128/91‑1 (MQ=255)                                                                              ttGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACggg          >  1:2905430/1‑91 (MQ=255)                                                                                   aTAGGCATTATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTtgtg     >  1:808756/1‑91 (MQ=255)                                                                                   aTAGGCATTATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTtgtg     >  1:808835/1‑91 (MQ=255)                                                                                   aTAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTtgtg     <  1:3927618/91‑1 (MQ=255)                                                                                   aTAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTtgtg     <  1:3927569/91‑1 (MQ=255)                                                                                    tAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTgtgt    <  1:3082849/91‑1 (MQ=255)                                                                                    tAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTgtgt    <  1:133187/91‑1 (MQ=255)                                                                                    tAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTgtgt    <  1:3475691/91‑1 (MQ=255)                                                                                    tAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTgtgt    <  1:3475276/91‑1 (MQ=255)                                                                                      ggCATTATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTGTGTta  >  1:3236543/1‑91 (MQ=255)                                                                                           |                                                                                      TTCAAATTGTTGTAAAATTTCATCTGACATCTTGATTCCTGGCACTTCATTATGCAAAAAGAGTGCGTTTTTGTAACTTGCGATAGGCATAATGCCTATGAAAAATGGTTTGTTCAAGTGCTTAGTGGCATGGTAAATTTCAATGATTTTCTCTTTGCTGTACACGGGTTGTGTTA  >  USA300TCH1516_ALE/410374‑410549

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: ‑