Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,883,255	C→T	D159N (GAT→AAT)	dnaA ←	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,883,255	0	C	T	100.0%	195.0 / NA	51	D159N (GAT→AAT)	dnaA	chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/27);  total (24/27)

AACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATCCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGGC  >  NC_000913/3883109‑3883400                                                                                                                                                   |                                                                                                                                                  aaCAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGcc                                                                                                                                               >  2:829520/1‑151 (MQ=255)     aaGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCt                                                                                                                                           >  2:806524/1‑151 (MQ=255)      aGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTg                                                                                                                                          >  1:499291/1‑151 (MQ=255)        cgcTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGc                                                                                                                                        >  2:134072/1‑151 (MQ=255)          cTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCg                                                                                                                                       >  2:60390/1‑150 (MQ=255)               aGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAgccgc                                                                                                                                 >  1:65891/1‑151 (MQ=255)                   cATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCcgcg                                                                                                                             >  1:520116/1‑151 (MQ=255)                    atatAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCcgcgc                                                                                                                            >  2:52591/1‑151 (MQ=255)                    atatAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCcgcgc                                                                                                                            >  2:488665/1‑151 (MQ=255)                               tttGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTgg                                                                                                                 >  1:235967/1‑151 (MQ=255)                                ttGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTgg                                                                                                                 <  2:581279/150‑1 (MQ=255)                                  ggCATTCGGCTTGCGCGCAATAAGGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGt                                                                                                                <  2:89538/149‑1 (MQ=255)                                             tGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTc                                                                                                   >  2:78870/1‑151 (MQ=255)                                               cgcgcCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCaa                                                                                                 <  2:681945/151‑1 (MQ=255)                                               cgcgcCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCa                                                                                                  >  2:617739/1‑150 (MQ=255)                                                   ccATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGaa                                                                                             <  1:798051/151‑1 (MQ=255)                                                   ccATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGaa                                                                                             <  2:42976/151‑1 (MQ=255)                                                    cATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTAGAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAg                                                                                            <  1:93330/151‑1 (MQ=255)                                                       aaTGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGtt                                                                                          <  1:633973/150‑1 (MQ=255)                                                            cGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCaaa                                                                                    <  2:480634/151‑1 (MQ=255)                                                               tACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACgt                                                                                 >  1:332089/1‑151 (MQ=255)                                                               tACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACgt                                                                                 >  1:53451/1‑151 (MQ=255)                                                                 cccACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACgtgt                                                                               <  1:471851/151‑1 (MQ=255)                                                                    aCCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGtt                                                                            >  1:886575/1‑151 (MQ=255)                                                                     ccGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGttt                                                                           <  2:52684/151‑1 (MQ=255)                                                                            cagcagGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGttt                                                                    <  1:448942/151‑1 (MQ=255)                                                                            caacgggTGTGTTTTCCCCAAACCCGAGCCGCCAAAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCATCGAACTTATCAAACGTGTGTTTGACGttt                                                                    <  2:43583/146‑1 (MQ=255)                                                                             agcagGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTa                                                                   <  2:695814/151‑1 (MQ=255)                                                                                 ggTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGtt                                                               <  1:426328/151‑1 (MQ=255)                                                                                  gTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTa                                                              <  2:748744/151‑1 (MQ=255)                                                                                            cccAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAgg                                                    <  1:365454/151‑1 (MQ=255)                                                                                              cAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCTCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATa                                                      <  1:93153/147‑1 (MQ=255)                                                                                                gACCCGTGCCGCCATAAAGGAACAACGGGTTATAAGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCgg                                                >  1:233086/1‑151 (MQ=255)                                                                                                   ccGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTc                                             <  1:633063/151‑1 (MQ=255)                                                                                                    cGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTc                                             >  1:586512/1‑150 (MQ=255)                                                                                                     gTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCACCGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTg                                           >  2:505202/1‑151 (MQ=255)                                                                                                        ccgccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccg                                        <  1:411637/151‑1 (MQ=255)                                                                                                          gccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggg                                      <  1:149273/151‑1 (MQ=255)                                                                                                          gccATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggg                                      <  2:104353/151‑1 (MQ=255)                                                                                                             aTAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggcc                                   <  2:233060/151‑1 (MQ=255)                                                                                                               aaaGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggccg                                  <  2:787562/150‑1 (MQ=255)                                                                                                                 aGGAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTgccggggccggg                                >  2:192172/1‑150 (MQ=255)                                                                                                                  ggAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGAc                              <  1:20251/151‑1 (MQ=255)                                                                                                                   gAACAACGGGTTATAGGCACCGCCAGGGTTATTCGCCTCCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACg                             <  1:500614/151‑1 (MQ=255)                                                                                                                     acaacGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGtt                           <  1:437169/151‑1 (MQ=255)                                                                                                                      caacGGGTTATAGGCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGtt                           >  2:666179/1‑150 (MQ=255)                                                                                                                                  ggCACCGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAg              <  2:244177/151‑1 (MQ=255)                                                                                                                                     aCCGCCAGGGGTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGCAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGTCCGGGACGTTATCCCAACCTGAgcgc           >  2:315677/1‑151 (MQ=255)                                                                                                                                       cGCCAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGt         >  2:765594/1‑151 (MQ=255)                                                                                                                                         ccAGGGTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTTTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGt         >  2:40777/1‑149 (MQ=255)                                                                                                                                              gTTATTCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGgc  >  2:556993/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                  AACAAAGCGCTCGGAGTGCATATAAACCACTTTGGCATTCGGCTTGCGCGCCATAATGCCGTTACCCACCGCATGCAGCAGGTGAGTTTTACCCAGACCCGTGCCGCCATAAAGGAACAACGGGTTATAGGCACCGCCAGGGTTATCCGCCACCTGGCGAGCCGCCGCGCGCGCCAGTTGGTTAGATTTACCTTCAACGAAGTTATCAAACGTGTGTTTGACGTTTACGTTAGAACGATAGGTCGGTTCTGCCGGGGCCGGGACGTTATCCCAACCTGAGCGCGTAGAAGGC  >  NC_000913/3883109‑3883400

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑