BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,158,202	+C	coding (961/975 nt)	ygiRQ ←	Fe‑S oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,158,201	1	.	C	99.3%	387.9 / ‑4.4	147	coding (962/975 nt)	ygiRQ	Fe‑S oxidoreductase
Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (71/75); total (72/75)
Fisher's exact test for biased strand distribution p-value = 4.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

Only 100 of 155 total aligned reads displayed.

GGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑CTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTTCTC  >  NC_000913/3158126‑3158271

 gTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACCTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑c                                                                       >  1:2907646/1‑76 (MQ=255)

 gTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑c                                                                       <  2:1835653/76‑1 (MQ=255)

   aGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑cct                                                                     >  1:3502863/1‑74 (MQ=255)

    gAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑cctg                                                                    <  2:1932832/76‑4 (MQ=255)

        gCGGTATATCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCGCAGCCTGggtt                                                                 <  1:4886479/76‑1 (MQ=255)

        gCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggtt                                                                 <  1:2169200/76‑1 (MQ=255)

         cGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttg                                                                <  1:5788011/76‑1 (MQ=255)

          ggAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttgg                                                               >  1:1008576/1‑76 (MQ=255)

          ggAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑cct                                                                     <  1:4364878/69‑3 (MQ=255)

          ggAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑cct                                                                     >  2:4364877/1‑67 (MQ=255)

           gAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                                                              >  2:661579/1‑76 (MQ=255)

           gAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGggttggt                                                              <  1:736206/76‑1 (MQ=255)

           gAATAGCAGGCGGGATGATCCACACATAGCGGCCGCCGTGTTTTTGAATCAATGCGCGGGCACAGCCTGggttggt                                                              >  1:3210698/1‑76 (MQ=255)

            aaTAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACCGCCTGggttggtt                                                             >  2:1493997/1‑76 (MQ=255)

             aTAGCAGGCGGGTTGATCCACACCTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTCGGttt                                                            >  2:5677564/1‑76 (MQ=255)

             aTAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGttt                                                            <  2:4149261/76‑1 (MQ=255)

             aTAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGttt                                                            <  2:5378598/76‑1 (MQ=255)

              tAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGtttg                                                           >  1:750963/1‑75 (MQ=255)

              tAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTc                                                           <  1:5226200/76‑1 (MQ=255)

                 cAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCgtg                                                        <  1:2311719/76‑1 (MQ=255)

                    gCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCgtggtg                                                     <  1:2429507/76‑1 (MQ=255)

                    gCGGGTTGACCCGCACACAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCgtggtg                                                     <  1:943622/76‑1 (MQ=255)

                     cGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGc                                                    <  2:3435735/76‑1 (MQ=255)

                      gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCCCAGCCTGGGTTGGTTTCGTGGCGCa                                                   >  2:263818/1‑76 (MQ=255)

                      gggTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGcg                                                   >  1:895541/1‑75 (MQ=255)

                        gTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGa                                                 >  2:2011693/1‑76 (MQ=255)

                         ttGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGaa                                                >  1:3285857/1‑76 (MQ=255)

                         ttGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGaa                                                <  1:4560694/76‑1 (MQ=255)

                          tGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAAt                                               <  2:3963857/76‑1 (MQ=255)

                          tGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAAt                                               <  1:4672231/76‑1 (MQ=255)

                          tGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAAt                                               >  2:905863/1‑76 (MQ=255)

                          tGAGCCACACATGGCGGTCGCCGGGTTTTGGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAAt                                               <  2:4004565/76‑1 (MQ=255)

                           gATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATa                                              >  1:5799871/1‑76 (MQ=255)

                             tCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcg                                            >  2:3720031/1‑76 (MQ=255)

                             tCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcg                                            >  1:1525454/1‑76 (MQ=255)

                             tCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcg                                            <  2:3638366/76‑1 (MQ=255)

                             tCCACACATAGCGGCCGCCGTGTTTTTGCATCAATGCGCGGGCACACCCTGGGTTGGTTTCGTGGGGCAGAATAcg                                            >  2:3199879/1‑76 (MQ=255)

                              gcacacaGAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcgc                                           <  2:2738029/75‑1 (MQ=255)

                              ccACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcgc                                           <  1:1136966/76‑1 (MQ=255)

                              ccACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGGGCAGAATAcgc                                           >  2:5345881/1‑76 (MQ=255)

                               cacacaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcgcg                                          >  2:2798388/1‑76 (MQ=255)

                               cacacaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATAcgcg                                          <  1:1362435/76‑1 (MQ=255)

                                acacaGAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCGCAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGa                                         <  2:4440935/76‑1 (MQ=255)

                                  acaTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAg                                       >  2:3646767/1‑76 (MQ=255)

                                   caTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGc                                      <  1:4554239/76‑1 (MQ=255)

                                    aTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGcc                                     >  2:5559790/1‑75 (MQ=255)

                                    aTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCa                                     >  1:2404492/1‑76 (MQ=255)

                                    aTAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCa                                     >  2:3665821/1‑76 (MQ=255)

                                      aGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGCGGTGCAGAATACGCGAAGCATg                                   >  2:5115195/1‑76 (MQ=255)

                                        cGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATggg                                 <  1:2307108/76‑1 (MQ=255)

                                         ggTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGc                                <  1:2795581/76‑1 (MQ=255)

                                          gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCg                               >  1:2634001/1‑76 (MQ=255)

                                          gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCg                               <  2:1334636/76‑1 (MQ=255)

                                          gTCGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCg                               <  1:1112298/76‑1 (MQ=255)

                                            cGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTa                             <  2:5011739/76‑1 (MQ=255)

                                            cGCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTa                             >  1:5101080/1‑76 (MQ=255)

                                             gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTAc                            <  1:2156563/76‑1 (MQ=255)

                                             gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTAc                            >  2:393084/1‑76 (MQ=255)

                                             gCCGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTAc                            <  1:2620492/76‑1 (MQ=255)

                                               cGTGTTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCGGAATACGCGAAGCATGGGCGTACAg                          <  2:172225/76‑1 (MQ=255)

                                                gtgtTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGc                         >  1:3081409/1‑76 (MQ=255)

                                                gtgtTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGc                         <  2:3210698/76‑1 (MQ=255)

                                                 tgtTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCCTGGGCGTACAGCa                        >  2:3516682/1‑76 (MQ=255)

                                                 tgtTTTTGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCa                        >  1:1692676/1‑76 (MQ=255)

                                                     tttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACttt                    <  1:2031357/76‑1 (MQ=255)

                                                     tttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACttt                    <  2:3180535/76‑1 (MQ=255)

                                                     tttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACttt                    <  2:5388476/76‑1 (MQ=255)

                                                     tttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACttt                    <  2:5453219/76‑1 (MQ=255)

                                                     tttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACttt                    <  1:1019618/76‑1 (MQ=255)

                                                      ttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGACGCATGGGCGCACAGCCCTTTa                   >  2:5102377/1‑76 (MQ=255)

                                                      ttGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTa                   <  2:5735473/76‑1 (MQ=255)

                                                       tGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTAt                  >  1:1824770/1‑76 (MQ=255)

                                                       tGCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTAt                  >  1:3408874/1‑76 (MQ=255)

                                                        gCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATc                 <  1:5347996/76‑1 (MQ=255)

                                                        gCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATc                 <  1:5282429/76‑1 (MQ=255)

                                                        gCATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATc                 <  2:611627/76‑1 (MQ=255)

                                                         cATCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCg                <  1:468225/76‑1 (MQ=255)

                                                          aTCAATGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGc               >  2:4974508/1‑76 (MQ=255)

                                                             aaTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCt            >  1:3792160/1‑76 (MQ=255)

                                                             aaTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCt            >  2:1309262/1‑76 (MQ=255)

                                                             aaTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCt            >  2:1964189/1‑76 (MQ=255)

                                                              aTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATGCGCGCAGCATTGTCGTACAGCACTTTCTCGCCCtt           <  1:2975493/76‑1 (MQ=255)

                                                              aTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCtt           <  1:5232318/76‑1 (MQ=255)

                                                              aTGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCtt           <  2:4948941/76‑1 (MQ=255)

                                                               tGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGGGAAGCATGGGCGTACAGCACTTTATCGCCCTTc          <  2:1879390/76‑1 (MQ=255)

                                                               tGCGCGGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTc          <  1:1381433/76‑1 (MQ=255)

                                                                  gcgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACt       >  1:4936793/1‑76 (MQ=255)

                                                                  gcgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACt       <  1:2934529/76‑1 (MQ=255)

                                                                  gcgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACt       >  2:2598175/1‑76 (MQ=255)

                                                                  gcgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACt       <  2:2151036/76‑1 (MQ=255)

                                                                  gcaggCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACt       >  2:4050274/4‑76 (MQ=255)

                                                                   cgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACCGCACTTTATCGCCCTTCACtt      >  2:315140/1‑76 (MQ=255)

                                                                   cgGGCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACtt      >  2:2547861/1‑76 (MQ=255)

                                                                    gggCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACttt     >  1:1792721/1‑76 (MQ=255)

                                                                    gggCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACttt     >  2:3125452/1‑76 (MQ=255)

                                                                    gggCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACtt      >  2:3091531/1‑75 (MQ=255)

                                                                      gCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTtct   <  2:4202657/76‑1 (MQ=255)

                                                                      gCACAGCCTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTtct   <  1:3611059/76‑1 (MQ=255)

                                                                      gCACAGCCTGGGTTGGTTTCGTGGCGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTtct   >  2:3041591/1‑76 (MQ=255)

                                                                       cacaGCCTGGGTTGGTTTGGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTtctc  <  2:2101121/76‑1 (MQ=255)

GGTAGAAAGCGGAATAGCAGGCGGGTTGATCCACACATAGCGGTCGCCGTGTTTTTGCATCAATGCGCGGGCACAG‑CTGGGTTGGTTTCGTGGTGCAGAATACGCGAAGCATGGGCGTACAGCACTTTATCGCCCTTCACTTTCTC  >  NC_000913/3158126‑3158271

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 9 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`