BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,679,168	T→C	7.6%	intergenic (+40/‑349)	USA300HOU_RS13790 → / → ssaA2_4	hypothetical protein/Staphylococcal secretory antigen ssaA2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,679,168	0	T	C	7.6%	622.3 / 31.8	212	intergenic (+40/‑349)	USA300HOU_RS13790/ssaA2_4	hypothetical protein/Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand): ref base T (94/101); new base C (2/15); total (96/116)
Fisher's exact test for biased strand distribution p-value = 4.16e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

Only 100 of 222 total aligned reads displayed.

GTAATTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCTTT  >  USA300TCH1516_ALE/2679078‑2679257

 tAATTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGCTACATGAATACATGGAGTCACATCATCTCATGTTAGCGctc                                                                                          >  2:3483901/1‑91 (MQ=255)

 tAATTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGctc                                                                                          >  2:713985/1‑91 (MQ=255)

 tAATTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGctc                                                                                          >  1:662666/1‑91 (MQ=255)

  acagaaaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGACACATCATCTCATGTTAGCGccct                                                                                         <  2:1172711/87‑1 (MQ=255)

  aaTTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGctct                                                                                         >  1:2263838/1‑91 (MQ=255)

   aTTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCGTGTTAGCGCTCTg                                                                                        <  1:57289/91‑1 (MQ=255)

   aTTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTg                                                                                        <  2:216752/91‑1 (MQ=255)

    ttAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGa                                                                                       >  2:857749/1‑91 (MQ=255)

     tAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGAt                                                                                      <  2:269618/91‑1 (MQ=255)

      aaaCGGGCACTATCAGTTTTCAACCAATTCACAACTGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaa                                                                                     <  1:3554703/91‑4 (MQ=255)

      aaaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGAtt                                                                                     >  1:345649/1‑91 (MQ=255)

      aaaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGAtt                                                                                     >  1:1257787/1‑91 (MQ=255)

      aaaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaa                                                                                     <  2:2360067/91‑4 (MQ=255)

       aaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTg                                                                                    >  1:1905831/1‑91 (MQ=255)

       aaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaat                                                                                    <  2:1640576/91‑5 (MQ=255)

       aaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaat                                                                                    <  2:431206/91‑5 (MQ=255)

       aaCGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaat                                                                                    <  1:2206953/91‑5 (MQ=255)

       aaCGGGCACTATCAGTTATCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCCCTgcaat                                                                                    <  1:3392712/91‑5 (MQ=255)

         cGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCa                                                                                  <  2:1422339/91‑1 (MQ=255)

           ggCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAgg                                                                                >  2:3388598/1‑91 (MQ=255)

           ggCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAgg                                                                                <  1:1310333/91‑1 (MQ=255)

            gCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAggg                                                                               >  2:181078/1‑91 (MQ=255)

            gCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAggg                                                                               >  1:2991936/1‑91 (MQ=255)

               cTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGgcgc                                                                            >  1:1552757/1‑91 (MQ=255)

                tATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCt                                                                           >  2:1269875/1‑91 (MQ=255)

                 aTCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTa                                                                          >  1:2362323/1‑91 (MQ=255)

                  tCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAt                                                                         >  2:1760526/1‑91 (MQ=255)

                   cAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAtt                                                                        >  1:3737286/1‑91 (MQ=255)

                   cAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAtt                                                                        <  2:2278736/91‑1 (MQ=255)

                    aGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAttt                                                                       <  1:3930843/91‑1 (MQ=255)

                     gTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAtttt                                                                      >  1:2087563/1‑91 (MQ=255)

                     gTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAtttt                                                                      >  2:771093/1‑91 (MQ=255)

                      ttttCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTAttttt                                                                     >  2:2854333/1‑91 (MQ=255)

                       tttCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTa                                                                    <  2:2932142/91‑1 (MQ=255)

                        ttCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTaa                                                                   >  1:384404/1‑91 (MQ=255)

                        ttCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTaa                                                                   >  1:713795/1‑91 (MQ=255)

                         tCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAAt                                                                  <  2:2033707/91‑1 (MQ=255)

                          cAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATg                                                                 >  1:1431817/1‑91 (MQ=255)

                          cAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATg                                                                 <  2:3297848/91‑1 (MQ=255)

                           aaCCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGt                                                                <  2:709484/91‑1 (MQ=255)

                              cAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTAt                                                             <  1:2442845/91‑1 (MQ=255)

                               aaTTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTAtt                                                            >  1:2289349/1‑91 (MQ=255)

                                aTTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTg                                                           >  2:3220972/1‑91 (MQ=255)

                                 ttCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTATCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGc                                                          <  2:2345579/91‑1 (MQ=255)

                                   cacaAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTa                                                        <  1:3603335/91‑1 (MQ=255)

                                     caAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACa                                                      >  2:3484873/1‑91 (MQ=255)

                                     caAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACa                                                      >  2:1757971/1‑91 (MQ=255)

                                       aaTGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACAtt                                                    >  2:3382735/1‑91 (MQ=255)

                                        aTGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACAttt                                                   <  1:104998/91‑1 (MQ=255)

                                        aTGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACAttt                                                   <  2:3852880/91‑1 (MQ=255)

                                        aTGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTGATTGCTACAtgt                                                   <  2:613496/91‑3 (MQ=255)

                                         tGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTa                                                  <  1:905540/91‑1 (MQ=255)

                                         tGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTa                                                  <  2:3701451/91‑1 (MQ=255)

                                            aCAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTATGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGta                                               <  2:3058137/91‑1 (MQ=255)

                                             cAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGtat                                              >  1:855464/1‑91 (MQ=255)

                                              aaTGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGtata                                             <  2:2919308/91‑1 (MQ=255)

                                               aTGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTatat                                            >  1:2034179/1‑91 (MQ=255)

                                               aTGATACATGAACACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTatat                                            >  1:3025125/1‑91 (MQ=255)

                                                tGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATAtt                                           >  2:1986114/1‑91 (MQ=255)

                                                   tACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATtgtg                                        >  2:1938508/1‑91 (MQ=255)

                                                     cATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGAt                                      >  2:1550085/1‑91 (MQ=255)

                                                     cATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGAt                                      >  1:1666448/1‑91 (MQ=255)

                                                     cATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGAt                                      <  2:2213181/91‑1 (MQ=255)

                                                     cATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGAt                                      >  1:3269961/1‑91 (MQ=255)

                                                       tGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTg                                    >  1:417701/1‑91 (MQ=255)

                                                       tGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTg                                    <  2:2801262/91‑1 (MQ=255)

                                                       tGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTg                                    <  1:1668891/91‑1 (MQ=255)

                                                         aaTACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCt                                  <  1:2904346/91‑1 (MQ=255)

                                                           tACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTAt                                >  1:1330106/1‑91 (MQ=255)

                                                              aTGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTAtttt                             <  1:2583685/91‑1 (MQ=255)

                                                               tGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttc                            >  1:2732604/1‑91 (MQ=255)

                                                               tGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttc                            >  2:3087439/1‑91 (MQ=255)

                                                               tGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttc                            >  2:1406186/1‑91 (MQ=255)

                                                               tGGAGTCACATCATCTCATGTTAGCGCCCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttc                            >  2:2555730/1‑91 (MQ=255)

                                                                ggAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttct                           <  2:1723845/91‑1 (MQ=255)

                                                                 gAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttctt                          >  2:531352/1‑91 (MQ=255)

                                                                 gAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttctt                          <  1:1207998/91‑1 (MQ=255)

                                                                 gAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttctt                          >  1:1809308/1‑91 (MQ=255)

                                                                 gAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtttctt                          >  2:2589570/1‑91 (MQ=255)

                                                                 gAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATtctctt                          >  1:3300937/1‑91 (MQ=255)

                                                                      acaTCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGt                     <  1:1497618/91‑1 (MQ=255)

                                                                        atcatcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTGTTTTCTTTCAGTta                   <  2:3361438/91‑1 (MQ=255)

                                                                         tcatcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTtat                  <  1:46902/91‑1 (MQ=255)

                                                                         tcatcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTtat                  <  2:250134/91‑1 (MQ=255)

                                                                         tcagcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTtat                  <  1:3066746/91‑1 (MQ=255)

                                                                           atcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAg                >  1:361585/1‑91 (MQ=255)

                                                                           atcTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAg                <  1:321447/91‑1 (MQ=255)

                                                                               cATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAAct            >  2:3929851/1‑90 (MQ=255)

                                                                               cATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAAcc            >  2:1218419/1‑91 (MQ=255)

                                                                                  gTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATg         >  1:14525/1‑91 (MQ=255)

                                                                                    tAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTa       <  2:1341683/91‑1 (MQ=255)

                                                                                    tAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTa       <  1:1587613/91‑1 (MQ=255)

                                                                                     aGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTAc      <  2:3955917/91‑1 (MQ=255)

                                                                                     aGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTAc      <  1:2576646/91‑1 (MQ=255)

                                                                                     aGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTAc      <  2:2431698/91‑1 (MQ=255)

                                                                                      gcgcTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTCTATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTAcc     >  2:1011939/1‑91 (MQ=255)

                                                                                       cgcTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCt    <  2:3025290/91‑1 (MQ=255)

                                                                                        gcTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCtt   <  1:2785190/91‑1 (MQ=255)

                                                                                         ctctGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCttt  <  1:3518206/91‑1 (MQ=255)

                                                                                         ctctGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCttt  >  2:2973528/1‑91 (MQ=255)

GTAATTAAACGGGCACTATCAGTTTTCAACCAATTCACAAATGTACAATGATACATGAATACATGGAGTCACATCATCTCATGTTAGCGCTCTGATTGCAGGGCGCTATTTTTAATGTTATTGCTACATTTAGTATATTGTGATTGCTATTTTCTTTCAGTTATAGAACCATGTACCTTT  >  USA300TCH1516_ALE/2679078‑2679257

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: `‑`