Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,796,146	C→T	A158V (GCG→GTG)	csiR →	transcriptional repressor of csiD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,796,146	0	C	T	100.0%	177.6 / NA	55	A158V (GCG→GTG)	csiR	transcriptional repressor of csiD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/25);  total (30/25)

AGCTTGAGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCG  >  NC_000913/2796011‑2796281                                                                                                                                         |                                                                                                                                        aGCTTGAGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTggtggc                                                                                                                                      <  1:1404173/139‑1 (MQ=255)       aGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGgtggcg                                                                                                                                     >  2:1730367/1‑134 (MQ=255)       aGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGgtggcg                                                                                                                                     <  1:1730367/134‑1 (MQ=255)       aGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTa                                                                                                                                >  1:951704/1‑139 (MQ=255)       aGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTa                                                                                                                                >  2:1374512/1‑139 (MQ=255)                    cAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTgg                                                                                                                   >  1:428639/1‑139 (MQ=255)                           aaaaTGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAGCGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTgcggc                                                                                                            <  1:1600945/139‑1 (MQ=255)                               tGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAAc                                                                                                        <  2:951704/139‑1 (MQ=255)                                     atgaGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCt                                                                                                  >  1:679978/1‑139 (MQ=255)                                          tGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCg                                                                                                                             >  2:1489206/1‑107 (MQ=255)                                          tGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCg                                                                                                                             <  1:1489206/107‑1 (MQ=255)                                          tGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGaa                                                                                                         <  1:133319/127‑1 (MQ=255)                                          tGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGaa                                                                                                         >  2:133319/1‑127 (MQ=255)                                           gggATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTAt                                                                                                                       >  2:1003274/1‑112 (MQ=255)                                           gggATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTAt                                                                                                                       <  1:1003274/112‑1 (MQ=255)                                                 tGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAAt                                                                                      >  2:8561/1‑139 (MQ=255)                                                   cGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTgg                                                                                          <  2:792033/133‑1 (MQ=255)                                                   cGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTgg                                                                                          >  1:792033/1‑133 (MQ=255)                                                   cGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGc                                                                                    >  2:1256663/1‑139 (MQ=255)                                                    gTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCt                                                                                   <  1:615002/139‑1 (MQ=255)                                                     tcatcaGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTg                                                                                  >  2:673281/1‑139 (MQ=255)                                                        tcaGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACg                                                                                                       >  1:1276762/1‑115 (MQ=255)                                                        tcaGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACg                                                                                                       <  2:1276762/115‑1 (MQ=255)                                                             cGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATaa                                                                          <  1:8561/139‑1 (MQ=255)                                                               tttCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGTGGAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATaaa                                                                         >  2:407302/1‑139 (MQ=255)                                                                 tCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGTGGAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAaca                                                                       <  1:407302/139‑1 (MQ=255)                                                                    tACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGAt                                                                   <  2:679978/139‑1 (MQ=255)                                                                       ggCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAg                                                                >  2:375293/1‑139 (MQ=255)                                                                          aaTTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCAc                                                             >  1:442105/1‑139 (MQ=255)                                                                               tgGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGAc                                                        >  2:1662200/1‑139 (MQ=255)                                                                                 gCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGtt                                                                                                                                 >  1:1458424/1‑64 (MQ=255)                                                                                 gCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGtt                                                                                                                                 <  2:1458424/64‑1 (MQ=255)                                                                                   gggCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTgg                                                                                          <  1:931905/101‑1 (MQ=255)                                                                                   gggCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTgg                                                                                          >  2:931905/1‑101 (MQ=255)                                                                                   gggCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTg                                                    >  2:1596757/1‑139 (MQ=255)                                                                                     gCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGAc                                                  <  1:1256663/139‑1 (MQ=255)                                                                                              ctcACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGa                                                                                                          <  2:1028121/74‑1 (MQ=255)                                                                                              ctcACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGa                                                                                                          >  1:1028121/1‑74 (MQ=255)                                                                                                cACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTAc                                       <  1:1662200/139‑1 (MQ=255)                                                                                                   tATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCt                                                                                                                 <  1:1009235/62‑1 (MQ=255)                                                                                                   tATTAGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCt                                                                                                                 >  2:1009235/1‑62 (MQ=255)                                                                                                     tttGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGgcg                                  >  2:366487/1‑139 (MQ=255)                                                                                                        gctgcAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTggagga                                                                             >  2:1524740/1‑93 (MQ=255)                                                                                                        gctgcAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTggagga                                                                             <  1:1524740/93‑1 (MQ=255)                                                                                                           gcAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGAc                                                  <  2:1098503/117‑1 (MQ=255)                                                                                                           gcAAATGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGAc                                                  >  1:1098503/1‑117 (MQ=255)                                                                                                             aaaTGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGATGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATAc                          >  1:1006536/1‑139 (MQ=255)                                                                                                               aTGCGT‑GAACGGTTGTTTGATCTGGTGGCGCGTTATCGAt                                                                                                                           >  1:962196/1‑40 (MQ=39)                                                                                                               aTGCGT‑GAACGGTTGTTTGATATGGTGGCGCGTTATCGAt                                                                                                                           <  2:962196/40‑1 (MQ=37)                                                                                                                   gT‑GAACGGTTGTTTGATCTTGTGGGGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAAGGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACcgcgcg                    <  1:1596757/139‑1 (MQ=255)                                                                                                                      gAACGGTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACcgcgcgcg                  <  1:375293/139‑1 (MQ=255)                                                                                                                          ggTTGTTTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAg              >  2:303264/1‑139 (MQ=255)                                                                                                                            ttgttTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAaca                                                                       <  1:89825/80‑1 (MQ=255)                                                                                                                            ttgttTGATCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAaca                                                                       >  2:89825/1‑80 (MQ=255)                                                                                                                                    tCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTc                                                                                               >  2:525283/1‑48 (MQ=255)                                                                                                                                    tCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTc                                                                                               <  1:525283/48‑1 (MQ=255)                                                                                                                                    tCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCt                                                                                   <  2:1669952/60‑1 (MQ=255)                                                                                                                                    tCTGGTGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCt                                                                                   >  1:1669952/1‑60 (MQ=255)                                                                                                                                      tggtggCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATgcg  >  2:1678270/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                        AGCTTGAGGCCTGTGACGCCAGCGAGAAAATGCTTGATGAGTGGGATCTGCGTCATCAGGCGTTTCATACGGCAATTGTGGCGGGCTGTGGTTCTCACTATTTGCTGCAAATGCGT‑GAACGGTTGTTTGATCTGGCGGCGCGTTATCGATTTATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCG  >  NC_000913/2796011‑2796281

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑