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	91.8%	212.0 / 8.8	74	A146T (GCC→ACC)	yaeF	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (4/2);  new base T (33/34);  total (38/36)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.52e-01

GAGAACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAACGAT  >  NC_000913/216471‑216667                                                                                                  |                                                                                                    gagaACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTaa                                                                                                   <  2:1781113/100‑1 (MQ=255)  agaACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTaaa                                                                                                  >  2:145999/1‑100 (MQ=255)   gaACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAAc                                                                                                 <  2:449753/100‑1 (MQ=255)     aCGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAAcgc                                                                                               <  1:1165913/100‑1 (MQ=255)      cGGATTCAGTGCACACATCTGGCGAGTCACCATAAAAGGAATAAATTCGACAATACCGCGATAGTTATAACCGATATCTTTGACTTTATTGCAAAAcg                                                                                                >  1:180829/1‑98 (MQ=255)      cGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAAcgcg                                                                                              >  1:180976/1‑100 (MQ=255)      cGGATTCAGGGAGCACATCTGGCGAGTCACCATAAACGCAATAACTTCGACAGTGCCGCGATAGTTATAACCGCTACCTTTGATTTTATTGCTAAAcgcg                                                                                              >  1:1648413/1‑100 (MQ=255)        gATTCAGTGAGCACATCTGGCGAGCCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGt                                                                                            >  2:910253/1‑100 (MQ=255)         aTTCAGTGAGGACATCTGGGGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTg                                                                                           <  1:838229/100‑1 (MQ=255)         aTTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTg                                                                                           <  1:1344674/100‑1 (MQ=255)         aTTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTg                                                                                           <  1:1011842/100‑1 (MQ=255)          ttCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGa                                                                                          <  1:870790/100‑1 (MQ=255)           tCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGat                                                                                         <  1:504423/100‑1 (MQ=255)            cAGTGAGCACATCTGGCGAGTCAGCATAAAGGGATTACATTCGACACTGCCGCGATAGTTATAACCGCTAGCTTTGATTTTATTGGTAAACGCGGTGa                                                                                          >  1:964028/1‑98 (MQ=255)            cAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGata                                                                                        >  2:1836328/1‑100 (MQ=255)              gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGTCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATc                                                                                      <  1:1246986/100‑1 (MQ=255)              gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATc                                                                                      >  1:797623/1‑100 (MQ=255)              gTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATc                                                                                      <  1:667157/100‑1 (MQ=255)                gAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCtg                                                                                    <  1:1248891/100‑1 (MQ=255)                gAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCtg                                                                                    >  1:1891761/1‑100 (MQ=255)                    acaTCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGc                                                                                <  2:440114/100‑1 (MQ=255)                     caTCTGGCGAGTCACCATAAAGGGAATAAATTCAACAATGCCGCGATAGTTATAACCGCTATCTTTGATTATATTGGTAAACACAGTGATATCtatg                                                                                  >  1:1171661/1‑97 (MQ=255)                       tCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttg                                                                             <  1:92032/100‑1 (MQ=255)                        cTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgt                                                                            <  2:1896405/100‑1 (MQ=255)                         tGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgtt                                                                           >  1:968187/1‑100 (MQ=255)                          ggCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgttg                                                                          >  1:1080005/1‑100 (MQ=255)                          ggCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCttgttg                                                                          >  1:1721134/1‑100 (MQ=255)                             gAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCgg                                                                       <  1:130724/100‑1 (MQ=255)                              aGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCggg                                                                      <  2:619644/100‑1 (MQ=255)                                    cATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGa                                                                >  1:1315560/1‑100 (MQ=255)                                    cATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGa                                                                >  1:64360/1‑100 (MQ=255)                                     aTAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGAt                                                               >  1:90260/1‑100 (MQ=255)                                      tAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATc                                                              >  2:58552/1‑100 (MQ=255)                                          gggAACAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCgg                                                           <  2:339868/99‑1 (MQ=255)                                           ggAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGa                                                         >  1:20725/1‑100 (MQ=255)                                            gAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGAc                                                        <  2:1855845/100‑1 (MQ=255)                                               tAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCg                                                     <  2:1728887/100‑1 (MQ=255)                                                 aaTTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTa                                                   <  1:913087/100‑1 (MQ=255)                                                 aaTTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTa                                                   >  2:63342/1‑100 (MQ=255)                                                  aTTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTaa                                                  <  1:169473/100‑1 (MQ=255)                                                      gACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACg                                              <  2:497799/100‑1 (MQ=255)                                                          aTGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGaaaa                                          >  2:1162557/1‑100 (MQ=255)                                                          aTGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGaaaa                                          >  2:1137437/1‑100 (MQ=255)                                                           tGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAg                                         <  1:1620157/100‑1 (MQ=255)                                                             ccGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCt                                       <  2:1388455/100‑1 (MQ=255)                                                             ccGCGATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCt                                       >  2:460864/1‑100 (MQ=255)                                                               gcgATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGATGAAAAGCTTa                                     >  1:572770/1‑100 (MQ=255)                                                                cgATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTAt                                    >  2:1031306/1‑100 (MQ=255)                                                                 gATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATc                                   <  1:571970/100‑1 (MQ=255)                                                                 gATAGTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGCTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATc                                   <  2:646504/100‑1 (MQ=255)                                                                     gTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTa                               <  1:53157/100‑1 (MQ=255)                                                                     gTTATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTa                               <  1:331556/100‑1 (MQ=255)                                                                     gTTATAACCGCTAGCTTTGATTTTATTGGTAAACGCGGCGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTa                               >  1:1200503/1‑100 (MQ=255)                                                                      ttATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGTGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTAt                              <  1:93758/100‑1 (MQ=255)                                                                      ttATAACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTAt                              <  2:553350/100‑1 (MQ=255)                                                                         taACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCt                           >  2:946228/1‑100 (MQ=255)                                                                         taACCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCt                           >  1:868284/1‑100 (MQ=255)                                                                          aaCCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCtt                          >  1:242786/1‑100 (MQ=255)                                                                          aaCCGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCtt                          >  1:1870853/1‑100 (MQ=255)                                                                             cGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCAt                       >  1:1918425/1‑100 (MQ=255)                                                                             cGCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCAt                       >  2:146335/1‑100 (MQ=255)                                                                              gCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGACAAGCTTATCACTATGCTTCATc                      >  2:160926/1‑100 (MQ=255)                                                                              gCTATCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATc                      <  2:1870865/100‑1 (MQ=255)                                                                               cTAGCTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCg                     <  2:1672354/100‑1 (MQ=255)                                                                                tATCTTTGATTTTATAGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGc                    <  2:1918438/100‑1 (MQ=255)                                                                                   cTTTGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCttt                 >  2:1215497/1‑100 (MQ=255)                                                                                    tttGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCtttt                >  2:278547/1‑100 (MQ=255)                                                                                    tttGATTTTATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCtttt                >  1:878565/1‑100 (MQ=255)                                                                                         ttttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAg           >  2:1539315/1‑100 (MQ=255)                                                                                         ttttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAg           >  2:1933640/1‑100 (MQ=255)                                                                                         ttttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAg           <  1:402377/100‑1 (MQ=255)                                                                                          tttATTGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAgg          <  2:787560/100‑1 (MQ=255)                                                                                               tGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAAc     <  2:112627/100‑1 (MQ=255)                                                                                               tGGTAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAAc     >  1:662988/1‑100 (MQ=255)                                                                                                  cAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAATGGAAACGAt  <  2:64360/100‑1 (MQ=255)                                                                                                  |                                                                                                    GAGAACGGATTCAGTGAGCACATCTGGCGAGTCACCATAAAGGGAATAAATTCGACAATGCCGCGATAGTTATAACCGCTATCTTTGATTTTATTGGCAAACGCGGTGATATCTGTGGCTTGTTGCGGGGTAAGATCCGGGACTCGTAAGACGAAAAGCTTATCACTATGCTTCATCGCTTTTTTAAGGGAAACGAT  >  NC_000913/216471‑216667

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑