Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	88,159	G→T	E44D (GAG→GAT)	cra →	DNA‑binding transcriptional dual regulator Cra

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	88,159	0	G	T	100.0%	285.4 / NA	81	E44D (GAG→GAT)	cra	DNA‑binding transcriptional dual regulator Cra
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (54/27);  total (54/27)

CGTGTGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGAGCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTGGAC  >  NC_000913/88112‑88205                                                |                                               cGTGTGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATca                                              >  1:6484484/1‑50 (MQ=255)  gtgtGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATcac                                             <  1:1223115/50‑1 (MQ=255)  gtgtGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATca                                              >  1:2831243/1‑49 (MQ=255)  gtgtGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATca                                              >  1:1353471/1‑49 (MQ=255)  gtgtGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATca                                              >  1:2076935/1‑49 (MQ=255)  gtgtGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATca                                              >  1:2027947/1‑49 (MQ=255)    gtgAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACaa                                           >  1:2998209/1‑50 (MQ=255)     tgAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACaa                                           <  1:5885198/49‑1 (MQ=255)     tgAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAAt                                          >  1:1294024/1‑50 (MQ=255)     tgAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAAt                                          >  1:6007872/1‑50 (MQ=255)      gAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAAt                                          >  1:3558543/1‑49 (MQ=255)       aGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTa                                        <  1:4262999/50‑1 (MQ=255)       aGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTa                                        >  1:4368326/1‑50 (MQ=255)       aGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTa                                        <  1:3792490/50‑1 (MQ=255)       aGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTa                                        >  1:6655320/1‑50 (MQ=255)        gCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTac                                       <  1:476743/50‑1 (MQ=255)         cGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTac                                       >  1:6222635/1‑49 (MQ=255)         cGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTac                                       >  1:2731354/1‑49 (MQ=255)          gACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTacca                                     <  1:5243338/50‑1 (MQ=255)          gACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTacca                                     >  1:1345603/1‑50 (MQ=255)            cAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTaccacc                                   >  1:5842977/1‑50 (MQ=255)            cAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTaccacc                                   >  1:5451663/1‑50 (MQ=255)            cAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTaccacc                                   >  1:2736571/1‑50 (MQ=255)             aaaaCCGTTGAAAAAGTCATGGCTGTGGTGCTTGATCACAATTACCAccc                                  >  1:1665652/1‑50 (MQ=255)             aaaaCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCAccc                                  >  1:2379605/1‑50 (MQ=255)             aaaaCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCAccc                                  <  1:540675/50‑1 (MQ=255)              aaaCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCAccc                                  >  1:2053447/1‑49 (MQ=255)              aaaCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCg                                 <  1:4987426/50‑1 (MQ=255)                aCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGaa                               >  1:6592931/1‑50 (MQ=255)                aCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGaa                               >  1:2985954/1‑50 (MQ=255)                aCCGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGaa                               >  1:2858388/1‑50 (MQ=255)                 ccGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAAc                              >  1:1154217/1‑50 (MQ=255)                  cGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACg                             <  1:5816610/50‑1 (MQ=255)                  cGTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACg                             >  1:4425437/1‑50 (MQ=255)                   gTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGc                            >  1:4715480/1‑50 (MQ=255)                   gTTGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGc                            >  1:1256025/1‑50 (MQ=255)                    ttGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGcc                           <  1:4194215/50‑1 (MQ=255)                    ttGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGcc                           <  1:719113/50‑1 (MQ=255)                     tGAAAAAGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCg                          >  1:3653147/1‑50 (MQ=255)                        aaaaGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTgg                       >  1:6061566/1‑50 (MQ=255)                          aaGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCa                     <  1:2311372/50‑1 (MQ=255)                          aaGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCa                     <  1:2038277/50‑1 (MQ=255)                          aaGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCa                     <  1:5866424/50‑1 (MQ=255)                           aGTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAg                    <  1:84742/50‑1 (MQ=255)                            gTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGc                   >  1:1956717/1‑50 (MQ=255)                            gTCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGc                   >  1:6188424/1‑50 (MQ=255)                             tCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCt                  >  1:6747426/1‑50 (MQ=255)                             tCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCt                  >  1:547744/1‑50 (MQ=255)                             tCATGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCt                  >  1:2337051/1‑50 (MQ=255)                               aTGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTgg                >  1:612509/1‑50 (MQ=255)                               aTGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTgg                <  1:4183366/50‑1 (MQ=255)                                tGGCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTggg               >  1:1791234/1‑50 (MQ=255)                                 ggCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGc              >  1:5106088/1‑50 (MQ=255)                                 ggCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGc              >  1:5630348/1‑50 (MQ=255)                                 ggCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGc              >  1:2177292/1‑50 (MQ=255)                                  gCTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCt             >  1:5204141/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:3196495/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:6359344/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:6103442/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:2482126/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:4726082/1‑50 (MQ=255)                                   cTGTGGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCtt            >  1:4279409/1‑50 (MQ=255)                                    tgtgGTGCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           >  1:2153879/1‑50 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           <  1:3246113/48‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           <  1:1542131/48‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           <  1:460229/48‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           <  1:475688/48‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTc           <  1:1774611/48‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCg          <  1:1035750/49‑1 (MQ=255)                                      tggtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGt         >  1:4228464/1‑50 (MQ=255)                                        gtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGc       <  1:3174903/50‑1 (MQ=255)                                        gtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGc       >  1:6534143/1‑50 (MQ=255)                                        gtgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGc       >  1:1359531/1‑50 (MQ=255)                                         tgCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCt      <  1:1939625/50‑1 (MQ=255)                                          gCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTg     >  1:5837982/1‑50 (MQ=255)                                          gCGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTg     >  1:4227264/1‑50 (MQ=255)                                           cGTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTg     >  1:2005612/1‑49 (MQ=255)                                            gTGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTGGa   >  1:1243399/1‑50 (MQ=255)                                             tGATCACAATTACCACCCGGACGCCGTGGCAGCTGGGCTTCGTGCTGGAc  <  1:2669032/50‑1 (MQ=255)                                             tGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTGGAc  <  1:1548864/50‑1 (MQ=255)                                             tGATCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTGGAc  <  1:4222367/50‑1 (MQ=255)                                                |                                               CGTGTGAGCGACAAAACCGTTGAAAAAGTCATGGCTGTGGTGCGTGAGCACAATTACCACCCGAACGCCGTGGCAGCTGGGCTTCGTGCTGGAC  >  NC_000913/88112‑88205

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑