Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_007793	2,769,687	G→T	S90R (AGC→AGA)	nsaS ←	sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007793	2,769,687	0	G	T	100.0%	144.2 / NA	49	S90R (AGC→AGA)	nsaS	sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (2/47);  total (2/47)

GGCTCATCTCTTTCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTAGCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGCTTAT  >  NC_007793/2769613‑2769776                                                                           |                                                                                          ttccgaTCTCTTTCGAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATGCat                                                                  <  1:4209911/95‑2 (MQ=255) tcttccgatctTTCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCag                                                                  <  1:3782806/92‑2 (MQ=255)        tcttttCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTc                                                           <  1:4222070/97‑1 (MQ=255)        ctctTTTAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTc                                                           <  1:5641084/100‑1 (MQ=255)        ctctTTCTAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTc                                                           <  1:1751850/100‑1 (MQ=255)        ctctTTCGAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTc                                                           <  1:694383/100‑1 (MQ=255)        ctctTTCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTc                                                           <  1:4754326/100‑1 (MQ=255)          ctTTCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCag                                                         <  1:3737071/100‑2 (MQ=255)            ttCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCacgg                                                       <  1:314591/100‑4 (MQ=255)               aaGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTa                                                    <  1:993035/100‑1 (MQ=255)                  tAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGc                                                 <  1:1776295/100‑1 (MQ=255)                    aCAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTg                                               <  1:2106517/100‑1 (MQ=255)                    aCAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTg                                               <  1:2688263/100‑1 (MQ=255)                    aCAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTg                                               <  1:1249584/100‑1 (MQ=255)                    aCAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTg                                               <  1:5116807/100‑1 (MQ=255)                      aGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGag                                             <  1:3931447/100‑2 (MQ=255)                      aGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGAt                                             <  1:97178/100‑1 (MQ=255)                      aGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGAt                                             <  1:537626/100‑1 (MQ=255)                      aGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGAt                                             <  1:4288585/100‑1 (MQ=255)                       gTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGAtg                                            <  1:1632225/100‑2 (MQ=255)                       gTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATa                                            <  1:3645643/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTGTATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:492662/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:3174697/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:616676/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:2868864/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:4837524/100‑1 (MQ=255)                        ttGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATAc                                           <  1:1311421/100‑1 (MQ=255)                             ctgcAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGc                                      <  1:2931390/100‑1 (MQ=255)                                 aGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCAtta                                  <  1:1252582/100‑2 (MQ=255)                                     aTGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTa                              <  1:1041997/100‑1 (MQ=255)                                     aTGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTa                              <  1:2239792/100‑1 (MQ=255)                                            ttttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTc                       <  1:4448687/100‑1 (MQ=255)                                             tttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCa                      <  1:3771317/100‑1 (MQ=255)                                             tttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCa                      <  1:1048950/100‑1 (MQ=255)                                             tttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCa                      <  1:5306257/100‑1 (MQ=255)                                             tttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCa                      <  1:2028154/100‑1 (MQ=255)                                             tttCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCa                      <  1:294260/100‑1 (MQ=255)                                               tCATTTGATGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAAt                    <  1:2816520/100‑1 (MQ=255)                                                       tGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATttgttgtt            <  1:4151966/100‑1 (MQ=255)                                                       tGTACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATttgttgtt            <  1:5667578/100‑1 (MQ=255)                                                         tACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATttgttgttgt          >  1:5019892/1‑100 (MQ=255)                                                         tACCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATttgttgttgt          >  1:3313484/1‑100 (MQ=255)                                                          aCCCATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATttgttgttgtt         <  1:1760091/100‑1 (MQ=255)                                                            ccATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTgg       <  1:4980394/100‑1 (MQ=255)                                                            ccATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTgg       <  1:4513088/100‑1 (MQ=255)                                                             cATGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGc      <  1:3491008/100‑1 (MQ=255)                                                              aTGTTAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGCt     <  1:1877947/100‑1 (MQ=255)                                                               tGTTAAAAAGTATCTCTCTACATAATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGCtt    <  1:4799598/100‑1 (MQ=255)                                                                 ttAAAAAGTATCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGCTtat  <  1:2700524/100‑1 (MQ=255)                                                                           |                                                                                          GGCTCATCTCTTTCAAGTAACAGTTGTGCTGCAGTAATGGGTGTTTTCATTTGATGTACCCATGTTAAAAAGTAGCTCTCTACATCATTTTTATATTCAATTTGTTCATTTTTAAGCTGATACAACGCATTTTCTAAGTTTTCAATTTGTTGTTGTTGGCTTAT  >  NC_007793/2769613‑2769776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑