Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,712,518	(C)6→7	intergenic (+360/‑251)	nth → / → dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,712,512	1	.	C	100.0%	188.7 / NA	55	intergenic (+354/‑257)	nth/dtpA	DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (27/28);  total (27/28)

TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712377‑1712637                                                                                                                                         |                                                                                                                              tCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccc                                                                                                                            <  1:205019/139‑1 (MQ=255)   aGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  1:325345/139‑1 (MQ=255)     gTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccc                                                                                                                        >  1:1078850/1‑138 (MQ=255)                ttAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgcag                                                                                                              >  1:818558/1‑139 (MQ=255)                                          gACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTACCGTAACGtttttt                                                                                    >  2:971839/1‑139 (MQ=255)                                                  aaaCATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAtt                                                                            <  2:637559/139‑1 (MQ=255)                                                       ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:971839/139‑1 (MQ=255)                                                       ttACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:1325948/139‑1 (MQ=255)                                                        tACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGc                                                                      >  2:1437286/1‑139 (MQ=255)                                                         acacTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCt                                                                     >  1:323167/1‑139 (MQ=255)                                                            cTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGa                                                                  <  1:1053249/139‑1 (MQ=255)                                                               gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  1:1207358/1‑139 (MQ=255)                                                               gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  2:564665/1‑139 (MQ=255)                                                               gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATaa                                                               >  1:1180696/1‑139 (MQ=255)                                                               gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  2:1146036/79‑1 (MQ=255)                                                               gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  1:1146036/1‑79 (MQ=255)                                                               acTATTTTTCAGAAACTGGACTATCTAACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCACCACCCCCCCTCTCAGTGCAGTGAAAAAATCTACCGTCACGTGTTTTGAAAAATTTAACACTGGATaa                                                               >  1:30297/2‑139 (MQ=255)                                                                    ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  1:47369/1‑126 (MQ=255)                                                                    ttttCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAAAAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  2:47369/126‑1 (MQ=255)                                                                           aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGaa                                                   <  2:323167/139‑1 (MQ=255)                                                                                 gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTg                                             >  1:804899/1‑139 (MQ=255)                                                                                     aTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAAtt                                         >  2:526095/1‑139 (MQ=255)                                                                                      tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgc                                                                                                                >  2:1460196/1‑67 (MQ=255)                                                                                      tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgc                                                                                                                <  1:1460196/67‑1 (MQ=255)                                                                                      tctcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTc                                        <  1:1471357/139‑1 (MQ=255)                                                                                        tcACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTccc                                      <  1:1273244/139‑1 (MQ=255)                                                                                           cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccctct                                                                                                                     <  2:1249004/56‑5 (MQ=255)                                                                                           cTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccccctct                                                                                                                     >  1:1249004/1‑52 (MQ=255)                                                                                            tAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:153308/139‑1 (MQ=255)                                                                                             aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:1207358/139‑1 (MQ=255)                                                                                              gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATc                                                                                                    >  1:1126184/1‑71 (MQ=255)                                                                                              gTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATc                                                                                                    <  2:1126184/71‑1 (MQ=255)                                                                                                aaaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATATGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCGAGAATGGTTGAATTCCCCGCCTCAg                              >  1:1399269/1‑139 (MQ=255)                                                                                                 aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  1:805538/1‑45 (MQ=255)                                                                                                 aaaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  2:805538/45‑1 (MQ=255)                                                                                                  aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGtt                            <  1:526095/139‑1 (MQ=255)                                                                                                  aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          <  1:795516/44‑1 (MQ=255)                                                                                                  aaaCGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccccc                                                                                                                          >  2:795516/1‑44 (MQ=255)                                                                                                      gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAGATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  1:818290/1‑130 (MQ=255)                                                                                                      gCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:818290/130‑1 (MQ=255)                                                                                                          aaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  2:818558/139‑1 (MQ=255)                                                                                                                aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgca                                                                                                               <  2:1096352/42‑1 (MQ=255)                                                                                                                aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgca                                                                                                               >  1:1096352/1‑42 (MQ=255)                                                                                                                aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                   >  1:833592/1‑118 (MQ=255)                                                                                                                aGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGc                                   <  2:833592/118‑1 (MQ=255)                                                                                                                  aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGa                >  1:259743/1‑135 (MQ=255)                                                                                                                  aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGa                <  2:259743/135‑1 (MQ=255)                                                                                                                    cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    <  1:310509/129‑1 (MQ=255)                                                                                                                    cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTaa                    >  2:310509/1‑129 (MQ=255)                                                                                                                    cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGAttatta          >  1:757055/1‑139 (MQ=255)                                                                                                                      tatCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACa        <  1:564665/139‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         <  2:747234/71‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa                                                                         >  1:747234/1‑71 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       >  2:738763/1‑73 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg                                                                       <  1:738763/73‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTcc                                                        <  1:1296405/88‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTcc                                                        >  2:1296405/1‑88 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  2:16599/111‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 <  1:663665/111‑1 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  2:663665/1‑111 (MQ=255)                                                                                                                         cGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCt                                 >  1:16599/1‑111 (MQ=255)                                                                                                                            cGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGCAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAc  <  2:757055/139‑1 (MQ=255)                                                                                                                               tAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:1323239/104‑1 (MQ=255)                                                                                                                               tAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  >  1:1323239/1‑104 (MQ=255)                                                                                                                                aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  <  2:749633/103‑1 (MQ=255)                                                                                                                                aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGcc                                  >  1:749633/1‑103 (MQ=255)                                                                                                                                         |                                                                                                                              TCAGGTTAAAATCATTTAAATTTACACACGCAACAAATATTGACCTACAAAACATTACACTGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTTCCCGGAATGGTTGAATTCCCCGCCTCAGTTATATGTAACAGATTATTACAAAGGAC  >  NC_000913/1712377‑1712637

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑