Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	4,172,422	G→T	intergenic (‑23/‑96)	hdfR ← / → maoP	HTH‑type transcriptional regulator HdfR/macrodomain Ori organization protein MaoP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	4,172,422	0	G	T	100.0%	213.0 / NA	58	intergenic (‑23/‑96)	hdfR/maoP	HTH‑type transcriptional regulator HdfR/macrodomain Ori organization protein MaoP
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (30/28);  total (30/28)

AAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTAAC  >  NC_017635/4172375‑4172467                                                |                                              aaGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTc                                             <  1:1460407/50‑1 (MQ=255)   gTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGt                                           >  1:1147694/1‑50 (MQ=255)      tttAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCtttt                                         <  1:264746/49‑2 (MQ=255)      tttAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTAt                                        >  1:495498/1‑50 (MQ=255)      tttAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTAt                                        >  1:548296/1‑50 (MQ=255)       ttAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTAt                                        <  1:2057692/49‑1 (MQ=255)       ttAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTAt                                        >  1:964325/1‑49 (MQ=255)       ttAACAACTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTAt                                        <  2:1752841/49‑1 (MQ=38)         aaCAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGAt                                     >  2:512803/1‑50 (MQ=255)         aaCAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGAt                                     >  2:331628/1‑50 (MQ=255)          aCAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGAtt                                    >  1:1359315/1‑50 (MQ=255)           cAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGAttt                                   <  2:1105761/50‑1 (MQ=255)            aaTTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTa                                  <  2:1147720/50‑1 (MQ=255)            aaTTCCGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTa                                  <  1:1104064/50‑1 (MQ=255)                 cGTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtg                              <  2:1630526/49‑1 (MQ=255)                  gTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtt                            <  2:235143/50‑1 (MQ=255)                  gTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtt                            <  2:8846/50‑1 (MQ=255)                  gTATCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtt                            >  1:1417573/1‑50 (MQ=255)                    aTCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtttt                          >  2:1479241/1‑50 (MQ=255)                    aTCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtttt                          >  1:1303506/1‑50 (MQ=255)                    aTCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgtttt                          >  1:1243524/1‑50 (MQ=255)                     tCCACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttg                         <  1:438694/50‑1 (MQ=255)                      ccACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttgt                        >  1:496120/1‑50 (MQ=255)                      ccACAGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttgt                        >  1:1617557/1‑50 (MQ=255)                       cacaGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttgt                        <  1:1026084/49‑1 (MQ=255)                        acaGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttgttt                      >  2:1671689/1‑50 (MQ=255)                        acaGTGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAAtgttttgttt                      <  2:244156/50‑1 (MQ=255)                           gTGCTCTCCGCAAAATTATTTTTCGTTATGATCTAAATGTTTTGTTTTa                    >  1:59988/1‑49 (MQ=38)                            tGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTaca                  >  1:1405658/1‑50 (MQ=255)                            tGCTCTCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTaca                  <  1:1826204/50‑1 (MQ=255)                             gCTCTCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTacac                 >  1:1282625/1‑50 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTacac                 <  2:375082/49‑1 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACAct                >  2:1161718/1‑50 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACAct                >  1:1014242/1‑50 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACAct                <  2:111073/50‑1 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACAct                >  1:1739477/1‑50 (MQ=255)                              ctctCCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACAct                <  2:556814/50‑1 (MQ=255)                                 tcCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACActc               <  1:1516426/48‑1 (MQ=255)                                 tcCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACActc               <  2:1202091/48‑1 (MQ=255)                                 tcCGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACActc               <  1:715400/48‑1 (MQ=255)                                  ccGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGt            >  2:1807022/1‑50 (MQ=255)                                   cGCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTc           <  1:1975920/50‑1 (MQ=255)                                    gCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTc           >  2:1499553/1‑49 (MQ=255)                                    gCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCa          <  2:1657204/50‑1 (MQ=255)                                    gCAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCa          <  2:642619/50‑1 (MQ=255)                                     cAAAATTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCaa         <  2:686244/50‑1 (MQ=255)                                      aaaaTTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAg        >  2:1338743/1‑50 (MQ=255)                                      aaaaTTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAg        >  1:50439/1‑50 (MQ=255)                                      aaaaTTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAg        <  1:366251/50‑1 (MQ=255)                                       aaaTTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGc       >  2:828454/1‑50 (MQ=255)                                       aaaTTATTTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGc       >  1:1875686/1‑50 (MQ=255)                                         attattTTTCGTTATGCTTTAAATGTTTTGTTTTACACTCTGTCAAGCg      >  1:975601/1‑49 (MQ=255)                                         attattTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCg      >  1:1947999/1‑49 (MQ=255)                                         attattTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCg      >  1:708381/1‑49 (MQ=255)                                         attattTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGt     <  2:84174/50‑1 (MQ=255)                                            attTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTaa   <  1:1129378/49‑1 (MQ=255)                                            attTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTaa   <  2:1319778/49‑1 (MQ=255)                                            attTTTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTAAc  >  2:882556/1‑50 (MQ=255)                                             ttttTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTAAc  <  2:1230441/49‑1 (MQ=255)                                             ttttTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTAAc  <  2:1358327/49‑1 (MQ=255)                                                |                                              AAGTTTTTAACAATTCCGTATCCACAGTGCTCTCCGCAAAATTATTTGTCGTTATGATTTAAATGTTTTGTTTTACACTCTGTCAAGCGTAAC  >  NC_017635/4172375‑4172467

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑