Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,998,290	+G	coding (379/486 nt)	b4566 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,998,289	1	.	G	98.8%	225.0 / ‑3.5	85	coding (380/486 nt)	b4566	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (50/34);  total (51/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AATCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑G‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGATGTA  >  NC_000913/3998214‑3998359                                                                             |                                                                        aaTCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCa                                                                          >  2:4854257/1‑76 (MQ=255) aaTCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCa                                                                          >  1:561899/1‑76 (MQ=255)  aTCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑g                                                                        <  2:2678589/76‑1 (MQ=255)  aTCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑g                                                                        <  1:2942253/76‑1 (MQ=255)  aTCTCTTTACTGGTGTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑g                                                                        <  2:2707483/76‑1 (MQ=255)    ctctTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑gga                                                                      >  1:3139539/1‑74 (MQ=255)     tctTTACTGGTTTTGAAGGCATGCAGACTAACGATGCCGCCTTTATCTCCCGCGCCATAAAACACGCCGCCA‑ggac                                                                     <  2:3441072/76‑4 (MQ=255)     tctTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑ggac                                                                     <  1:4395298/76‑4 (MQ=255)     tctTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑ggac                                                                     <  2:3139539/76‑4 (MQ=255)        ttACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGa                                                                  <  1:1766982/76‑1 (MQ=255)        ttACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGa                                                                  <  1:1792361/76‑1 (MQ=255)         tccTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCGCCCGCGACATAAAACACGCCGCCAGG‑ACGGAt                                                                 <  1:1716698/74‑1 (MQ=255)          aCTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATa                                                                >  2:1300539/1‑76 (MQ=255)          aCTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATa                                                                <  1:3613887/76‑1 (MQ=255)           cTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATaa                                                               >  1:4820148/1‑76 (MQ=255)           cTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATaa                                                               >  2:447687/1‑76 (MQ=255)            tGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATaaa                                                              >  1:2887789/1‑76 (MQ=255)            tGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATaaa                                                              <  1:663827/76‑1 (MQ=255)             ggTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAg                                                             <  1:1734019/76‑1 (MQ=255)               ttttGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGaa                                                           >  1:4258986/1‑76 (MQ=255)               ttttGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGaa                                                           <  1:3966148/76‑1 (MQ=255)                tttGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGaaa                                                          <  1:4702995/76‑1 (MQ=255)                tttGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGaaa                                                          >  1:4841884/1‑76 (MQ=255)                  tGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAAtt                                                        <  2:4311486/76‑1 (MQ=255)                   gAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTc                                                       >  2:2615303/1‑76 (MQ=255)                      ggCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCt                                                    <  2:3350982/76‑1 (MQ=255)                       gCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCtt                                                   >  2:4171994/1‑76 (MQ=255)                        cATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTc                                                  >  2:1087799/1‑76 (MQ=255)                         aTCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCa                                                 >  1:3364925/1‑76 (MQ=255)                         aTCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCa                                                 <  2:2862889/76‑1 (MQ=255)                          tCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCAc                                                <  2:2377637/76‑1 (MQ=255)                          cccAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCAc                                                <  2:2412454/75‑1 (MQ=255)                              gACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCt                                              >  2:4650277/1‑74 (MQ=255)                              gACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCt                                              <  1:4650277/74‑1 (MQ=255)                              gACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGa                                            <  2:3315733/76‑1 (MQ=255)                               acgaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGaa                                           >  1:4250601/1‑76 (MQ=255)                                cgaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAg                                          <  2:2229152/76‑1 (MQ=255)                                cgaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAg                                          >  2:4384588/1‑76 (MQ=255)                                cgaacgaTGCCGACTGTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAg                                          <  1:4030876/76‑1 (MQ=255)                                 gaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGc                                         >  2:1508420/1‑76 (MQ=255)                                 gaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGc                                         >  1:3406235/1‑76 (MQ=255)                                 gaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGc                                         >  2:3810058/1‑76 (MQ=255)                                 gaacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGc                                         >  2:4389241/1‑76 (MQ=255)                                  aaggaTGCCGCCTTTATCTCCCGCGACATAAAACACGCGTCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCg                                        <  2:4436403/73‑1 (MQ=255)                                  aacgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCg                                        >  2:264164/1‑76 (MQ=255)                                   acgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCga                                       >  1:4548297/1‑76 (MQ=255)                                   acgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCga                                       <  1:3185633/76‑1 (MQ=255)                                   acgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCga                                       >  2:3973129/1‑76 (MQ=255)                                   acgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCga                                       >  2:2136399/1‑76 (MQ=255)                                    nnaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGCAGCgag                                      >  1:1071042/3‑76 (MQ=255)                                    cgaTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCgag                                      <  1:4713479/76‑1 (MQ=255)                                      aTGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGAt                                    >  1:1396109/1‑76 (MQ=255)                                       tGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGAtt                                   >  2:752699/1‑76 (MQ=255)                                        gCCGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGAttt                                  >  2:4051429/1‑76 (MQ=255)                                         ccGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTa                                 >  2:3685386/1‑76 (MQ=255)                                          cGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTaa                                >  1:181713/1‑76 (MQ=255)                                          cGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTaa                                >  2:2355125/1‑76 (MQ=255)                                          cGACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTaa                                >  2:3678113/1‑76 (MQ=255)                                          cGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑GTACTGATAAATCCATTCCCTTCACCTGAAGCGAGACTTaa                                >  2:2365624/1‑76 (MQ=255)                                           gACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAAc                               >  1:2811975/1‑76 (MQ=255)                                           gACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAAc                               <  1:1123835/76‑1 (MQ=255)                                           gACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAAc                               <  1:3642159/76‑1 (MQ=255)                                           gACTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAAc                               <  1:4482346/76‑1 (MQ=255)                                            aCTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACg                              <  1:1834943/76‑1 (MQ=255)                                            aCTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACg                              <  1:2900942/76‑1 (MQ=255)                                             cTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGc                             >  1:868336/1‑76 (MQ=255)                                             cTTTATCTCCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGc                             >  1:623849/1‑76 (MQ=255)                                                   ctcCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCtt                       >  1:2405623/1‑76 (MQ=255)                                                    tcCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTc                      <  1:150893/76‑1 (MQ=255)                                                    tcCCGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTc                      >  2:682663/1‑76 (MQ=255)                                                    ccccGCGACAGAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTc                      <  1:198096/75‑1 (MQ=255)                                                     cccGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTct                     >  1:4665605/1‑76 (MQ=255)                                                      ccGCGACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTctg                    >  1:2030253/1‑76 (MQ=255)                                                        gcgACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTctgct                  <  2:3102535/76‑1 (MQ=255)                                                        gcgACATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTctgct                  >  1:6036/1‑76 (MQ=255)                                                           aCATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGAc               >  2:4781031/1‑76 (MQ=255)                                                            cATAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGAcc              <  1:595033/76‑1 (MQ=255)                                                             aTAAAACACGCCGCCAGG‑ACGGATAAAGAAATTCCTTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCg             >  1:2971050/1‑76 (MQ=255)                                                               aaacCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGtt           <  1:2042057/76‑1 (MQ=255)                                                               aaaaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGtt           <  2:1401037/76‑1 (MQ=255)                                                               aaaaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGtt           >  2:3922545/1‑76 (MQ=255)                                                                aaaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCAACTTCTGCTGACCGttt          >  1:2674421/1‑76 (MQ=255)                                                                 aaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGtttt         >  1:509466/1‑76 (MQ=255)                                                                 aaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGtttt         >  1:535485/1‑76 (MQ=255)                                                                 aaCACGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCCGCTGACCGtttt         >  2:51327/1‑76 (MQ=255)                                                                  acgcgccgcCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTc        <  2:2040685/73‑1 (MQ=255)                                                                   cacGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCg       >  2:4124330/1‑76 (MQ=255)                                                                    acGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCgc      >  2:550371/1‑75 (MQ=255)                                                                    acGCCGCCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGa      >  1:2374005/1‑76 (MQ=255)                                                                     cgccgcCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGAt     <  1:2293960/76‑1 (MQ=255)                                                                     cgccgcCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGAt     >  2:2218871/1‑76 (MQ=255)                                                                     cgccgcCAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGAt     >  2:3428557/1‑76 (MQ=255)                                                                      gccgccAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGATg    >  2:2914452/1‑76 (MQ=255)                                                                        cgccAGG‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGATGTa  <  2:2312891/76‑1 (MQ=255)                                                                             |                                                                        AATCTCTTTACTGGTTTTGAAGGCATCCAGACGAACGATGCCGACTTTATCTCCCGCGACATAAAACACGCCGCCA‑G‑ACGGATAAAGAAATTCCCTTCACCTGAAGCGAGATTTAACGCCACCTTCTGCTGACCGTTTTCGATGTA  >  NC_000913/3998214‑3998359

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑