Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	362,884	A→G	L99S (TTA→TCA)	lacY ←	lactose permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	362,884	0	A	G	98.6%	249.8 / ‑4.5	71	L99S (TTA→TCA)	lacY	lactose permease
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (38/32);  total (39/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

TCTCAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTAACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCAG  >  NC_000913/362789‑362980                                                                                                |                                                                                                 tctcAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAg                                                                                              <  1:713786/100‑1 (MQ=255)  ctcAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGt                                                                                             >  1:562565/1‑100 (MQ=255)    cAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTgg                                                                                           >  2:1124903/1‑100 (MQ=255)    cAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTgg                                                                                           >  2:1133177/1‑100 (MQ=255)        aaaTGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCg                                                                                       <  2:662304/100‑1 (MQ=255)         cttGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGa                                                                                      <  1:1280982/98‑1 (MQ=255)          tcttccgatctgctgGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGaa                                                                                     <  2:1031850/91‑1 (MQ=255)          aTGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGaa                                                                                     <  2:506702/100‑1 (MQ=255)          aTGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGaa                                                                                     <  1:336963/100‑1 (MQ=255)           tGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAg                                                                                    <  1:1426813/100‑1 (MQ=255)           tGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAg                                                                                    >  2:1280977/1‑100 (MQ=255)           tGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAg                                                                                    <  2:566178/100‑1 (MQ=255)            gCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGa                                                                                   >  2:188243/1‑100 (MQ=255)                ctACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATaaa                                                                               >  2:245190/1‑100 (MQ=255)                   ctgctgGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAAt                                                                            >  1:530309/1‑100 (MQ=255)                       tgGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAGATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAg                                                                        <  1:721427/100‑1 (MQ=255)                        ggCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATGAAGa                                                                       <  1:729879/100‑1 (MQ=255)                         gcgcACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGaa                                                                      >  1:444763/1‑100 (MQ=255)                          cgcACCGGCGTTAAAACAAAAACCTAGATAAAAACCACCAACAATAGATCCTACTACAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGaa                                                                      >  2:376732/1‑99 (MQ=255)                            cACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACgg                                                                   >  1:38439/1‑100 (MQ=255)                            cACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACgg                                                                   >  2:569281/1‑100 (MQ=255)                              ccGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGgcg                                                                 <  2:1154904/100‑1 (MQ=255)                              ccGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGgcg                                                                 <  2:699848/100‑1 (MQ=255)                               cGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGgcgc                                                                <  1:471788/100‑1 (MQ=255)                                 gCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCaa                                                              <  1:263593/100‑1 (MQ=255)                                  cGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCaaa                                                             >  1:469396/1‑100 (MQ=255)                                   gTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACATTGGCCCGAAGATAAAAATAAAGAACGGCGCAAAc                                                            >  1:1322530/1‑100 (MQ=255)                                      aaaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATc                                                         <  2:119123/100‑1 (MQ=255)                                      aaaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATc                                                         >  1:463494/1‑100 (MQ=255)                                      aaaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATc                                                         <  1:572482/100‑1 (MQ=255)                                       aaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCa                                                        >  2:1387604/1‑100 (MQ=255)                                       aaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCa                                                        <  1:112320/100‑1 (MQ=255)                                       aaaCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTAACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCa                                                        >  2:489260/1‑100 (MQ=255)                                         aCAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGTCGCAAACATCACt                                                      >  1:101242/1‑100 (MQ=255)                                               gCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGACGCAAACATCACTAACATg                                                >  1:1030345/1‑100 (MQ=255)                                                 ttccgatcttACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGcc                                              <  2:210273/91‑1 (MQ=255)                                                 cTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGcc                                              <  1:1468720/100‑1 (MQ=255)                                                  tAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCg                                             <  1:230675/100‑1 (MQ=255)                                                   aGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCgg                                            <  1:1424965/100‑1 (MQ=255)                                                     aTAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGta                                          <  1:1083534/100‑1 (MQ=255)                                                     aTAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGta                                          >  2:938059/1‑100 (MQ=255)                                                      tAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGtaa                                         >  1:854911/1‑100 (MQ=255)                                                         aTACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGtaataa                                      >  1:627501/1‑100 (MQ=255)                                                         aTACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGtaataa                                      >  2:435645/1‑100 (MQ=255)                                                         aTACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGtaataa                                      >  2:336997/1‑100 (MQ=255)                                                         aTACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGtaataa                                      >  1:604416/1‑100 (MQ=255)                                                          tACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGccagatcggaa                                     >  1:210273/1‑91 (MQ=255)                                                          tACCACCAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTaataat                                     <  2:376883/100‑1 (MQ=255)                                                           accaccAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATc                                    <  1:682146/100‑1 (MQ=255)                                                           accaccAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATc                                    <  1:89648/100‑1 (MQ=255)                                                           accaccAACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATc                                    <  1:891436/100‑1 (MQ=255)                                                            ccacaaACAATCGATACTAATAAAATGATGCATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACGAACATGCCGGTAATAATcc                                   <  2:128770/100‑1 (MQ=255)                                                             caccaACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCca                                  >  2:1559976/1‑100 (MQ=255)                                                              accaACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCcac                                 >  2:904510/1‑100 (MQ=255)                                                              accaACAATCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCcac                                 <  1:133933/100‑1 (MQ=255)                                                                 aacaaTCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCAcagc                              <  1:1281324/100‑1 (MQ=255)                                                                   caaTCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCAcagcag                            >  1:715518/1‑100 (MQ=255)                                                                   caaTCGATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCAcagcag                            >  2:863235/1‑100 (MQ=255)                                                                        gATCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTAtt                       >  1:603546/1‑100 (MQ=255)                                                                         aTCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTAttt                      >  1:184700/1‑100 (MQ=255)                                                                          tCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTg                     <  1:188243/100‑1 (MQ=255)                                                                          tCCTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTg                     <  2:469917/100‑1 (MQ=255)                                                                           ccTACTAAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTgc                    >  1:1540525/1‑100 (MQ=255)                                                                            ctactaAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTgcg                   >  2:1154950/1‑100 (MQ=255)                                                                             tactaAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTgcgc                  >  1:1187197/1‑100 (MQ=255)                                                                               ctaAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAg                >  1:1316343/1‑100 (MQ=255)                                                                               ctaAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAg                >  2:774360/1‑100 (MQ=255)                                                                               ctaAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAg                >  1:1190753/1‑100 (MQ=255)                                                                                taAAATGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGc               <  2:28913/100‑1 (MQ=255)                                                                                 aaaaTGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGcc              >  2:840125/1‑100 (MQ=255)                                                                                 aaaaTGTTGTATTGTGACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGcc              >  2:432265/1‑100 (MQ=255)                                                                                       ttgtattgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGtt        >  2:1032933/1‑100 (MQ=255)                                                                                       ttgtattgtaACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGtt        <  1:489261/100‑1 (MQ=255)                                                                                         gtattgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTg      <  1:863240/100‑1 (MQ=255)                                                                                          tattgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGt     >  2:361811/1‑100 (MQ=255)                                                                                           attgtgACAGTGGCCCGCAGATAAAAATAAAGAACGACGCAAACATCACTAACCTGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGt         >  2:1469526/1‑95 (MQ=255)                                                                                           attgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGTCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTc    <  2:562564/100‑1 (MQ=255)                                                                                           attgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTc    <  2:463039/100‑1 (MQ=255)                                                                                            ttgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCa   <  1:904515/100‑1 (MQ=255)                                                                                             tgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCAg  >  1:1232722/1‑100 (MQ=255)                                                                                             tgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCAg  >  1:112418/1‑100 (MQ=255)                                                                                             tgtgACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCAg  <  2:968545/100‑1 (MQ=255)                                                                                                |                                                                                                 TCTCAATAAATGCCTCTACTGCTGGCGCACCGGCGTTAAAACAAAAGCCTAGATAAATACCACCAACAATCGATCCTACTAAAATGTTGTATTGTAACAGTGGCCCGAAGATAAAAATAAAGAACGGCGCAAACATCACTAACATGCCGGTAATAATCCACAGCAGGTATTTGCGCAGCCCGAGTTTGTCAG  >  NC_000913/362789‑362980

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑