Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,202,604	C→T	R227C (CGC→TGC)	zraS →	sensory histidine kinase in two‑component regulatory system with ZraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,202,604	0	C	T	100.0%	154.7 / NA	46	R227C (CGC→TGC)	zraS	sensory histidine kinase in two‑component regulatory system with ZraR
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (22/24);  total (22/24)

TTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGCGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTAACCCACTTTCCTCGATTAAAGGACTGGCGAAATA  >  NC_000913/4202469‑4202731                                                                                                                                        |                                                                                                                                tttATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCt                                                                                                                              <  1:1117847/139‑1 (MQ=255)     tCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTcgcg                                                                                                                          <  1:131239/139‑1 (MQ=255)     tCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTcgcg                                                                                                                          <  1:894665/139‑1 (MQ=255)     tCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTcgcg                                                                                                                          <  1:39421/139‑1 (MQ=255)         cGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAg                                                                                                                      >  1:528354/1‑139 (MQ=255)           ttGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCt                                                                                                                    >  2:705521/1‑139 (MQ=255)                 ccAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACa                                                                                                              <  2:291336/139‑1 (MQ=255)                 ccAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACa                                                                                                              <  2:528354/139‑1 (MQ=255)                   aGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAg                                                                                                            <  2:981467/139‑1 (MQ=255)                         cTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTcgcg                                                                                                                          <  1:311701/119‑1 (MQ=255)                         cTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTcgcg                                                                                                                          >  2:311701/1‑119 (MQ=255)                                cAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAgcg                                                                                               <  2:971233/139‑1 (MQ=255)                                 aaCCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCt                                                                                                                              <  1:462053/107‑1 (MQ=255)                                 aaCCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCt                                                                                                                              >  2:462053/1‑107 (MQ=255)                                 aaCCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAgcgc                                                                                              >  2:191575/1‑139 (MQ=255)                                       gagTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCAGGCGACGGTGTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAagag                                                                                        >  2:761941/1‑139 (MQ=255)                                            gggAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCt                                                                                   >  2:359788/1‑139 (MQ=255)                                                  aGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGgc                                                                             >  2:448754/1‑139 (MQ=255)                                                              tGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCACGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCt                                                                 >  2:958301/1‑139 (MQ=255)                                                                 ttATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTAc                                                                                                               <  2:88093/90‑1 (MQ=255)                                                                 ttATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTAc                                                                                                               >  1:88093/1‑90 (MQ=255)                                                                   aTCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCgg                                                            >  2:1164136/1‑139 (MQ=255)                                                                    tCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGc                                                           <  2:655900/139‑1 (MQ=255)                                                                    tCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGc                                                           <  1:812197/139‑1 (MQ=255)                                                                     ccTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCa                                                          >  1:37333/1‑139 (MQ=255)                                                                      ctctTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAg                                                         >  1:466944/1‑139 (MQ=255)                                                                         ttCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCg                                                      <  1:1024889/139‑1 (MQ=255)                                                                         ttCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCg                                                      >  2:180905/1‑139 (MQ=255)                                                                         ttCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCAGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGct                                                      <  1:761941/139‑2 (MQ=255)                                                                          tCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGt                                                     >  2:668092/1‑139 (MQ=255)                                                                              ccTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGcc                                                 >  2:367676/1‑139 (MQ=255)                                                                                tGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACa                                                                                                              <  1:106256/76‑1 (MQ=255)                                                                                tGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACa                                                                                                              >  2:106256/1‑76 (MQ=255)                                                                                         tCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCg                                      <  1:705521/139‑1 (MQ=255)                                                                                           ttGCTGGCAAGCGTATTGTCAGTCTTCGGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTa                                    <  1:191575/139‑1 (MQ=255)                                                                                            tGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAaga                                                                                         <  2:371262/85‑1 (MQ=255)                                                                                            tGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAaga                                                                                         >  1:371262/1‑85 (MQ=255)                                                                                                   aaGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCg                                      >  1:248756/1‑129 (MQ=255)                                                                                                   aaGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCg                                      <  2:248756/129‑1 (MQ=255)                                                                                                     gCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGTGGCAGGCGTTg                                                   >  1:1025501/1‑114 (MQ=255)                                                                                                     gCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGTGGCAGGCGTTg                                                   <  2:1025501/114‑1 (MQ=255)                                                                                                        tATTGTCATTCTTCTGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTAACCCACTTTCCTc                       <  2:1226435/139‑1 (MQ=255)                                                                                                                    tctGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGatgaaatg                                                                                                    >  2:619730/1‑50 (MQ=255)                                                                                                                    tctGGTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGatgaaatg                                                                                                    <  1:619730/50‑1 (MQ=255)                                                                                                                        gTATCGCCGCTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTAACCCACTTTCCTCGATTAAAGGACTGGCg       <  2:466944/139‑1 (MQ=255)                                                                                                                             gccgcTATCTGTGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTAACCCACTTTCCTCGATTAAAGGACTGGCGAAATa  >  1:53025/1‑139 (MQ=255)                                                                                                                                        |                                                                                                                                TTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCCCTGGCGACGGTCTTGCTGGCAAGCGTATTGTCATTCTTCTGGTATCGCCGCTATCTGCGCTCGCGCCAGCTTCTACAAGATGAAATGAAGCGCAAAGAGAAGCTGGTGGCGCTGGGGCATCTTGCGGCAGGCGTTGCCCACGAAATCCGTAACCCACTTTCCTCGATTAAAGGACTGGCGAAATA  >  NC_000913/4202469‑4202731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑