Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,986	C→T	*275* (TAG→TAA)	gadX ←	acid resistance regulon transcriptional activator, autoactivator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,986	0	C	T	100.0%	212.2 / NA	66	*275* (TAG→TAA)	gadX	acid resistance regulon transcriptional activator, autoactivator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (37/29);  total (37/29)

ACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCATAATA  >  NC_000913/3664860‑3665120                                                                                                                                |                                                                                                                                       aCTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      >  2:464722/1‑129 (MQ=255)     aCTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcctt                                                                                                                        >  2:639994/1‑139 (MQ=255)       tGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      >  1:523281/1‑123 (MQ=255)           agCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑ATGCCGGG‑‑TTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                          <  1:626608/129‑1 (MQ=255)           agCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCC‑ATGCCGGG‑‑TTTTTTTATGTCTGAGTAAAACTTTATAATCTTAttcc                                                                                                                          >  2:626608/1‑129 (MQ=255)            gCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                                 >  2:1013073/1‑139 (MQ=255)             cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATGACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      <  2:779490/117‑1 (MQ=255)             cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      >  1:779490/1‑117 (MQ=255)             cacaAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGaa                                                                                                                >  1:521822/1‑139 (MQ=255)                aaaGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACgg                                                                                                             >  1:1152542/1‑139 (MQ=255)                            gCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTaa                                                                                                 >  2:695358/1‑139 (MQ=255)                                    ggAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                         <  1:655539/139‑1 (MQ=255)                                    ggAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTccc                                                                                         <  1:54473/139‑1 (MQ=255)                                       gtgtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTg                                                                                      <  1:639994/139‑1 (MQ=255)                                        tgtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgc                                                                                     >  2:443970/1‑139 (MQ=255)                                         gtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                                    >  2:597948/1‑139 (MQ=255)                                         gtTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcg                                                                                    <  2:928055/139‑1 (MQ=255)                                            ataACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGcaa                                                                                 <  1:290648/139‑1 (MQ=255)                                                cGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAAt                                                                             >  2:541191/1‑139 (MQ=255)                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAt                                                                                                                             >  2:732487/1‑89 (MQ=255)                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTAt                                                                                                                             <  1:732487/89‑1 (MQ=255)                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcgc                                                                                   >  1:544498/1‑131 (MQ=255)                                                  gTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTgcgc                                                                                   <  2:544498/131‑1 (MQ=255)                                                    ttattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      <  1:1414847/78‑1 (MQ=255)                                                     tattaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTta                                                                                                                                      >  1:1332476/1‑77 (MQ=255)                                                      attaGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTgc                                                                       <  1:597948/139‑1 (MQ=255)                                                             tGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAg                                                                >  2:1399987/1‑139 (MQ=255)                                                             tGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAg                                                                >  1:1118712/1‑139 (MQ=255)                                                                agaCGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                             <  1:1399987/139‑1 (MQ=255)                                                                    ggCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGt                                                         >  1:1252236/1‑139 (MQ=255)                                                                     gCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGtt                                                        >  1:276705/1‑139 (MQ=255)                                                                       aGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCg                                                      >  1:503645/1‑139 (MQ=255)                                                                         aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                                    <  2:503645/139‑1 (MQ=255)                                                                         aCTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                                    <  1:1013073/139‑1 (MQ=255)                                                                                  ttCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                            <  2:1279744/74‑1 (MQ=255)                                                                                  ttCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGt                                                                                                            >  1:1279744/1‑74 (MQ=255)                                                                                    cccGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                             >  2:628992/1‑119 (MQ=255)                                                                                    cccGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCa                                                             <  1:628992/119‑1 (MQ=255)                                                                                     ccGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGcc                                        >  1:1459296/1‑139 (MQ=255)                                                                                     ccGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGcc                                        >  1:675451/1‑139 (MQ=255)                                                                                       ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                      >  2:1017459/1‑139 (MQ=255)                                                                                       ggTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGa                                      >  1:511883/1‑139 (MQ=255)                                                                                         tCCCCTATGCCGGGTTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGAt                                     >  1:274016/1‑139 (MQ=255)                                                                                         tCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                    >  1:1015352/1‑139 (MQ=255)                                                                                         tCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                    <  1:443970/139‑1 (MQ=255)                                                                                           cccTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  <  2:1152542/139‑1 (MQ=255)                                                                                           cccTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  <  2:1005495/139‑1 (MQ=255)                                                                                           cccTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  <  2:124177/139‑1 (MQ=255)                                                                                             cTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTc                                <  1:695358/139‑1 (MQ=255)                                                                                              tATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                                    <  2:1110650/118‑1 (MQ=255)                                                                                              tATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGAc                                                    >  1:1110650/1‑118 (MQ=255)                                                                                                tGCCGGGTTTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCt                              <  2:274016/139‑1 (MQ=255)                                                                                                     gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATAct                        >  2:1119488/1‑139 (MQ=255)                                                                                                     gg‑TTTTTTTTATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAA‑GGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATActc                       >  1:1151420/1‑139 (MQ=255)                                                                                                           tttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                                 >  1:72095/1‑45 (MQ=255)                                                                                                           tttttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGa                                                                                                                 <  2:72095/45‑1 (MQ=255)                                                                                                             tttATGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTggg                 <  2:1015352/139‑1 (MQ=255)                                                                                                                aTGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGt              <  2:521822/139‑1 (MQ=255)                                                                                                                 tGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  >  2:1143379/1‑118 (MQ=255)                                                                                                                 tGTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  <  1:1143379/118‑1 (MQ=255)                                                                                                                  gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                    <  1:692251/115‑1 (MQ=255)                                                                                                                  gTCTGAGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATc                                    >  2:692251/1‑115 (MQ=255)                                                                                                                       aGTAAAACTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCTCTCCTGATACTCTGTGGGCGTCATCCCa       >  1:338838/1‑139 (MQ=255)                                                                                                                            aaCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  >  1:807763/1‑107 (MQ=255)                                                                                                                            aaCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGc                                  <  2:807763/107‑1 (MQ=255)                                                                                                                            aaCTTTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCataata  >  2:415905/1‑139 (MQ=255)                                                                                                                                |                                                                                                                                       ACTTACTGAGAGCACAAAGTTTCCCGTGCCAACAGGGAGTGTTATAACGGTTTATTAGTCTGGAGACGGCAGACTATCCTCTTCCCGGTCCCCTATGCCGGG‑TTTTTTTTATGTCTGAGTAAAACTCTATAATCTTATTCCTTCCGCAGAACGGTCAGTGCCGTAAAAATTCCCTTGCGCAACAATACTTGCCGCCGAGTCACGGTTCGACAATCTCTGCGCCGATCGCTCCTGATACTCTGTGGGCGTCATCCCATAATA  >  NC_000913/3664860‑3665120

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑