Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,796,296	C→T	T208M (ACG→ATG)	csiR →	transcriptional repressor of csiD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,796,296	0	C	T	100.0%	198.1 / NA	61	T208M (ACG→ATG)	csiR	transcriptional repressor of csiD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/34);  total (27/34)

ATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTA  >  NC_000913/2796163‑2796421                                                                                                                                      |                                                                                                                              aTCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCaa                                                                                                                          >  2:46641/1‑139 (MQ=255)  tCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCACCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGCGAGTTAATGCGCCAGCAGTTACTGATGCCAAt                                                                                                                         <  1:380725/139‑1 (MQ=255)        tGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCAt                                                                                                                   >  2:1007321/1‑139 (MQ=255)          cggcgAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 >  2:482419/1‑139 (MQ=255)               aaCGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCcag                                                                                                            <  1:1007321/139‑1 (MQ=255)               aaCGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCcag                                                                                                            <  1:1243963/139‑1 (MQ=255)                   gTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAgg                                                                                                        <  1:482419/139‑1 (MQ=255)                    tGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGc                                                                                                       >  2:1010245/1‑139 (MQ=255)                    tGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGc                                                                                                       >  2:749744/1‑139 (MQ=255)                            gTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 <  2:844024/121‑1 (MQ=255)                            gTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 >  1:844024/1‑121 (MQ=255)                               gAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            <  2:282669/139‑1 (MQ=255)                                 aaTGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              >  1:1381190/1‑135 (MQ=255)                                 aaTGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              <  2:1381190/135‑1 (MQ=255)                                       ggaggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAattaatta                                                                                    <  2:561071/139‑1 (MQ=255)                                       ggaggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAattaatta                                                                                    >  1:898336/1‑139 (MQ=255)                                         aggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAattact                                                                                  <  1:749744/139‑1 (MQ=255)                                         aggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAattact                                                                                  <  1:1010245/139‑1 (MQ=255)                                           gaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTActct                                                                                >  2:1549939/1‑139 (MQ=255)                                               aaCACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCg                                                                            <  1:1720008/139‑1 (MQ=255)                                               aaCACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCg                                                                            <  2:1495006/139‑1 (MQ=255)                                                        aGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCa                                                                   >  1:515762/1‑139 (MQ=255)                                                        aGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCa                                                                   <  2:1690598/139‑1 (MQ=255)                                                               gACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGa                                                                          >  1:831850/1‑125 (MQ=255)                                                               gACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGa                                                                          <  2:831850/125‑1 (MQ=255)                                                                 cccTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATCATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGcc                                                          <  1:46641/139‑1 (MQ=255)                                                                    tGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGc                                                           >  1:1553048/1‑135 (MQ=255)                                                                    tGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGc                                                           <  2:1553048/135‑1 (MQ=255)                                                                     gACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCgg                                                      >  2:145152/1‑139 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAAt                                                                                                                         >  1:1784343/1‑67 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAAt                                                                                                                         <  2:1784343/67‑1 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              <  2:752040/94‑1 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              >  1:752040/1‑94 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGc                                                                    <  1:1793294/120‑1 (MQ=255)                                                                          cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGc                                                                    >  2:1793294/1‑120 (MQ=255)                                                                                     gcgcGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGACTACGCAACGCTTGCCCCGGATAAATTTTATCCggg                                      <  1:954292/139‑1 (MQ=255)                                                                                               ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  2:898336/139‑1 (MQ=255)                                                                                               ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:715543/139‑1 (MQ=255)                                                                                               ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:236203/139‑1 (MQ=255)                                                                                                 gcgcgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATc                          <  2:318129/139‑1 (MQ=255)                                                                                                    cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGAt                                                    <  2:1087940/110‑1 (MQ=255)                                                                                                    cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGAt                                                    >  1:1087940/1‑110 (MQ=255)                                                                                                    cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGt                       >  1:93571/1‑139 (MQ=255)                                                                                                     gcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGtt                      >  2:343179/1‑139 (MQ=255)                                                                                                      cgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGttt                     >  1:1238915/1‑139 (MQ=255)                                                                                                                  aaTGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            >  2:1422788/1‑56 (MQ=255)                                                                                                                  aaTGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            <  1:1422788/56‑1 (MQ=255)                                                                                                                    tGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGa       <  2:515762/139‑1 (MQ=255)                                                                                                                      cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     >  2:1474219/1‑91 (MQ=255)                                                                                                                      cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     <  1:1474219/91‑1 (MQ=255)                                                                                                                      cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTAtt                  <  2:977537/126‑1 (MQ=255)                                                                                                                      cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTAtt                  >  1:977537/1‑126 (MQ=255)                                                                                                                        ccAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGAtttt   >  2:300289/1‑139 (MQ=255)                                                                                                                        ccAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGAtttt   >  2:660931/1‑139 (MQ=255)                                                                                                                         cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            >  2:596050/1‑113 (MQ=255)                                                                                                                         cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:596050/113‑1 (MQ=255)                                                                                                                         cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  2:1238915/139‑1 (MQ=255)                                                                                                                         cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  1:300289/139‑1 (MQ=255)                                                                                                                         cAGCATTTACTGATGCCAATTCCCAATATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTCATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  1:660931/139‑1 (MQ=255)                                                                                                                          aGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     >  2:408081/1‑87 (MQ=255)                                                                                                                          aGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     <  1:408081/87‑1 (MQ=255)                                                                                                                                      |                                                                                                                              ATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTA  >  NC_000913/2796163‑2796421

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: ‑