Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	1,440,480	C→T	K378K (AAG→AAA)	SAUSA300_RS07110 ←	two‑component sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	1,440,480	0	C	T	100.0%	148.8 / NA	55	K378K (AAG→AAA)	SAUSA300_RS07110	two‑component sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (4/51);  total (4/51)

AACGAGATTTATCCACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGCTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGATTAAAAATAATTGTTCGAATTG  >  NC_007793/1440383‑1440575                                                                                                  |                                                                                                aaCGAGATTTATCCACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGttt                                                                                               <  1:3340857/100‑1 (MQ=255)   cGAGATTTATCCACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTAt                                                                                             <  1:5019201/100‑1 (MQ=255)              cACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCtt                                                                                  <  1:2089990/100‑1 (MQ=255)               aCTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAGTTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTg                                                                                 <  1:2489995/100‑1 (MQ=255)               aCTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTg                                                                                 <  1:3492786/100‑1 (MQ=255)               aCTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTg                                                                                 <  1:522638/100‑1 (MQ=255)               aCTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTg                                                                                 <  1:5430919/100‑1 (MQ=255)               aCTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTA‑TTTTTGTTTATTTTTTAACCTTgc                                                                                <  1:598111/100‑2 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTgc                                                                                <  1:6607190/100‑2 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTgc                                                                                <  1:3580113/100‑2 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTga                                                                                <  1:2435434/100‑2 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTga                                                                                <  1:4721248/100‑2 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGt                                                                                <  1:3977562/100‑1 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGt                                                                                <  1:1237474/100‑1 (MQ=255)                cTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGt                                                                                <  1:5862367/100‑1 (MQ=255)                 tCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTgcg                                                                               <  1:6502693/100‑3 (MQ=255)                 tCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTgaa                                                                               <  1:4463205/100‑3 (MQ=255)                  cGATAAAAGCGATCAAAAATGAAATCTTGCTCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCt                                                                              <  1:5013724/100‑1 (MQ=255)                  cGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCt                                                                              <  1:2914559/100‑1 (MQ=255)                  cGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCt                                                                              <  1:3359126/100‑1 (MQ=255)                  cGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCt                                                                              <  1:4149258/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTTATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:2241041/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:1646293/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:5178307/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:5126325/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:1981948/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:3908189/100‑1 (MQ=255)                   gATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTACAATTATTTTTTGTTTATTTTTTAACCTTGTCtt                                                                             <  1:6575728/100‑1 (MQ=255)                                  aaaTGAAATCTTGGTCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCtt                                                              <  1:2568677/100‑1 (MQ=255)                                  aaaTGAAATCTTAATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCtt                                                              <  1:2294867/100‑1 (MQ=255)                                        tcttccgATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTCTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTAttctt                                                        <  1:3741280/94‑1 (MQ=255)                                        aaTCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTAttctt                                                        <  1:173363/100‑1 (MQ=255)                                         aTCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTAttcttc                                                       <  1:6606843/100‑1 (MQ=255)                                         aTCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTAttctta                                                       <  1:6269905/100‑2 (MQ=255)                                           cTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTcac                                                     <  1:1196123/100‑1 (MQ=255)                                             cgATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCCTATTCTTCAcat                                                   <  1:3465142/99‑1 (MQ=255)                                               aTCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCAcatca                                                 <  1:3165160/100‑1 (MQ=255)                                                tctcCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCAcatcat                                                <  1:429411/100‑1 (MQ=255)                                                tCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCAcatcat                                                <  1:5309322/100‑1 (MQ=255)                                                 cTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCata                                               <  1:229238/100‑1 (MQ=255)                                                  ttCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCatac                                              <  1:4038233/100‑2 (MQ=255)                                                    cttctGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATAttt                                            >  1:4398657/3‑100 (MQ=255)                                                          gAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCTCATCATATTTGATTGc                                      <  1:3631520/100‑1 (MQ=255)                                                             tACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCAtt                                   <  1:3729913/100‑1 (MQ=255)                                                             tACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCAtt                                   <  1:1092160/100‑1 (MQ=255)                                                             tACCAATTCCATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCAtg                                   <  1:4245500/100‑2 (MQ=255)                                                                tgctcttccgATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATc                                <  1:5094672/91‑1 (MQ=255)                                                                 gctcttccgATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCa                               <  1:3336884/92‑1 (MQ=255)                                                                    cttccgATCTGTATCTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCacgg                            <  1:4916811/95‑4 (MQ=255)                                                                     ccATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATaa                           <  1:3332442/100‑1 (MQ=255)                                                                     ccATGATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATaa                           <  1:4043515/100‑1 (MQ=255)                                                                        cgATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCaaggggcg                        <  1:5106173/99‑7 (MQ=255)                                                                         gATCTGTAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGAt                       >  1:1123743/1‑100 (MQ=255)                                                                             gctAATTTCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGATTaaa                   >  1:2612535/3‑100 (MQ=255)                                                                                   ttCAATTATTTTTTGTTTATTTTTTAACCTTGTCTTTACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGATTAAAaataat             >  1:3519696/1‑100 (MQ=255)                                                                                              tttGTTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTAATTGCATTATCAATAAAGATTAAAAATAATTGTTCGAATtg  <  1:1443976/100‑1 (MQ=255)                                                                                                  |                                                                                                AACGAGATTTATCCACTCGATAAAAGCGATCAAAAATGAAATCTTGATCTTCCTCTGGAATACCAATTCCATGATCTGTAATTTCAATTATTTTTTGCTTATTTTTTAACCTTGTCTTAACTTTAATTTTCTTATTCTTCACATCATATTTGATTGCATTATCAATAAAGATTAAAAATAATTGTTCGAATTG  >  NC_007793/1440383‑1440575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑