Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	216,568	C→T	A146T (GCC→ACC)	yaeF ←	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	216,568	0	C	T	98.7%	256.1 / ‑4.5	74	A146T (GCC→ACC)	yaeF	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (41/32);  total (42/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

AGAACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAACG  >  NC_000913/216472‑216665                                                                                                 |                                                                                                  agaACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTaaa                                                                                                <  1:394785/100‑1 (MQ=255)  gaACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAAc                                                                                               >  1:297667/1‑100 (MQ=255)     cGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAAcgcg                                                                                            >  1:1565536/1‑100 (MQ=255)       gATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGt                                                                                          <  2:1389203/100‑1 (MQ=255)        aTTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTg                                                                                         <  2:768785/100‑1 (MQ=255)        aTTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTg                                                                                         <  1:1493629/100‑1 (MQ=255)        aTTCAGTGAACACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTg                                                                                         <  2:972777/100‑1 (MQ=255)           cAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGata                                                                                      >  1:179132/1‑100 (MQ=255)            aGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGatat                                                                                     >  2:512372/1‑100 (MQ=255)            aGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGatat                                                                                     >  1:882222/1‑100 (MQ=255)             gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATc                                                                                    >  1:140448/1‑100 (MQ=255)             gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATc                                                                                    <  2:1299870/100‑1 (MQ=255)             gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATc                                                                                    <  2:1112284/100‑1 (MQ=255)             gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATc                                                                                    <  1:391345/100‑1 (MQ=255)                 tcacaTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGTTATCtgtg                                                                                >  2:699710/2‑100 (MQ=255)                    caTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCt                                                                             >  2:1314692/1‑100 (MQ=255)                    caTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCt                                                                             <  2:733576/100‑1 (MQ=255)                    caTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCt                                                                             >  2:755890/1‑100 (MQ=255)                    caTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCt                                                                             >  2:51157/1‑100 (MQ=255)                       cTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTCAACGCGGTGATATCTGTGGTttgt                                                                          >  2:1272287/1‑100 (MQ=255)                       cTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgt                                                                          <  2:1236305/100‑1 (MQ=255)                       cTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgt                                                                          >  2:770033/1‑100 (MQ=255)                       cTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgt                                                                          >  2:1570681/1‑100 (MQ=255)                        tGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgtt                                                                         >  1:564540/1‑100 (MQ=255)                            gAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCgg                                                                     <  1:770037/100‑1 (MQ=255)                            gAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCgg                                                                     <  1:480642/100‑1 (MQ=255)                                cACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTa                                                                 >  2:629141/1‑100 (MQ=255)                                 aCCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTaa                                                                >  2:903485/1‑100 (MQ=255)                                 aCCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTaa                                                                >  2:1129869/1‑100 (MQ=255)                                     tAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATc                                                            >  2:935047/1‑100 (MQ=255)                                      aaaGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATcc                                                           <  1:755124/100‑1 (MQ=255)                                         gggAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCggg                                                        >  1:1395111/1‑100 (MQ=255)                                          ggAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGa                                                       >  2:405834/1‑100 (MQ=255)                                          ggAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGa                                                       >  1:192964/1‑100 (MQ=255)                                          ggAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGa                                                       >  1:93174/1‑100 (MQ=255)                                           gAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGAc                                                      >  2:789034/1‑100 (MQ=255)                                           gAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGAc                                                      <  1:902722/100‑1 (MQ=255)                                                 aTTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTaa                                                <  1:789039/100‑1 (MQ=255)                                                  ttCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAg                                               >  2:461213/1‑100 (MQ=255)                                                  ttCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAg                                               >  2:763901/1‑100 (MQ=255)                                                   tCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGa                                              >  2:1416610/1‑100 (MQ=255)                                                       cAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGaa                                          <  1:877636/100‑1 (MQ=255)                                                        aaTGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGaaa                                         <  1:648400/100‑1 (MQ=255)                                                         aTGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGaaaa                                        >  2:1217647/1‑100 (MQ=255)                                                            ccGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCt                                     >  2:638284/1‑100 (MQ=255)                                                             cgcgATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCtt                                    <  2:82258/100‑1 (MQ=255)                                                              gcgATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTa                                   <  2:1513474/100‑1 (MQ=255)                                                               cgATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTAt                                  <  1:18963/100‑1 (MQ=255)                                                                  tAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCAc                               <  2:394629/100‑1 (MQ=255)                                                                    gTTATAGCTGCTATCTGTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATc                                 <  1:1421905/96‑1 (MQ=255)                                                                      tataACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGATTATCACTAt                            >  2:398043/1‑99 (MQ=255)                                                                       ataACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGc                          >  2:1140764/1‑100 (MQ=255)                                                                        taACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCt                         >  1:209803/1‑100 (MQ=255)                                                                        taACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCt                         >  2:1189100/1‑100 (MQ=255)                                                                          aCCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTc                       <  2:882215/100‑1 (MQ=255)                                                                            cGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCAt                     >  2:805485/1‑100 (MQ=255)                                                                            cGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCAt                     <  1:741151/100‑1 (MQ=255)                                                                              cTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAACTTATCACTATGCTTCATCg                   <  2:1413050/100‑1 (MQ=255)                                                                               tATCTTTGATTTTATTGGTAAACGCTGTCATATCTGTGGCTTGTTGCGGGTTAAGATCCGTGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGc                  <  2:1386106/100‑1 (MQ=255)                                                                                 tCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCtt                >  2:1322857/1‑100 (MQ=255)                                                                                  cTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCttt               >  1:390154/1‑100 (MQ=255)                                                                                  cTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAACACGAAAAGCTTATCACTATGCTTCATCGCttt               <  1:1491321/100‑1 (MQ=255)                                                                                   tttGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCtttt              >  2:1359003/1‑100 (MQ=255)                                                                                    ttGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCttttt             >  1:888308/1‑100 (MQ=255)                                                                                    ttGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCttttt             <  1:469492/100‑1 (MQ=255)                                                                                     tGATTTTAGTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCtttttt            <  2:660631/100‑1 (MQ=255)                                                                                      gATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTa           >  2:141877/1‑100 (MQ=255)                                                                                      gATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTa           <  2:912286/100‑1 (MQ=255)                                                                                       aTTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTaa          >  2:53757/1‑100 (MQ=255)                                                                                       aTTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTaa          <  2:1395101/100‑1 (MQ=255)                                                                                        ttttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCttttttt           >  2:1131680/1‑97 (MQ=255)                                                                                          ttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAggg       <  2:179132/100‑1 (MQ=255)                                                                                              tGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAAc   >  1:173973/1‑100 (MQ=255)                                                                                               ggCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAACg  >  2:885251/1‑100 (MQ=255)                                                                                                 |                                                                                                  AGAACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAACG  >  NC_000913/216472‑216665

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: ‑