Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	73,581	0	A	C	42.3%	83.0 / 12.7	52	V314G (GTA→GGA)	thiP	thiamine/thiamine pyrophosphate ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base A (22/8);  new base C (0/22);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 2.20e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCTTACTC  >  NC_000913/73435‑73730                                                                                                                                                     |                                                                                                                                                      gCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTAcc                                                                                                                                                     <  1:909971/149‑1 (MQ=255)  ccGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCa                                                                                                                                                  <  1:103881/151‑1 (MQ=255)    gcgcCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATc                                                                                                                                                >  2:271043/1‑151 (MQ=255)    gcgcCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATc                                                                                                                                                >  2:902822/1‑151 (MQ=255)     cgcCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATc                                                                                                                                                <  1:725588/150‑1 (MQ=255)       cccGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATcgac                                                                                                                                             <  2:864330/151‑1 (MQ=255)           cAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATc                                                                                                                                         >  1:688170/1‑151 (MQ=255)               tCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCAcc                                                                                                                                      <  1:270885/150‑1 (MQ=255)                cgcgACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGc                                                                                                                                    >  1:453030/1‑151 (MQ=255)                            aTAGCAGCATCAGGGCCAGCACTACGCAAAATCCCCCGGCCGCCGG‑CGCAATCCGCAACGGGGCCCACAGCGCCTGCCACAGCCCCGGTTGTGCCAGCACTCCCGGAAACGGGCG‑TTTTCCCCCATCGACGATCACCGCCAGt                                                                                                                                <  2:345434/143‑1 (MQ=255)                                        tGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAAcagc                                                                                                              >  1:79826/1‑149 (MQ=255)                                        tGGCCAGCACTCCGCACAATAC‑CCCGCCCCCAGTCCCATCACGCAAGGGCCCCCACGGCCCCTGCCACGGCACCGGTTGTCCCACCTCTTCCGGCAAC‑GGCGAATTTCCCCCTGCGCCGTTCACCGCCAGTAACGGTGgc                                                                                                                       <  1:928275/140‑1 (MQ=255)                                          gTCACCACTCCCCAAAATACCCCCGCCCCCAG‑GCCAATACGCAACGGGCTCCACAGCGCCTGCCACAGCCCCGGTTGTCCCAGCACTCCCGGCAACTGGCG‑ATTTCCCCCATCGACGATCGCCGCCAGTAACGGTGGCAGCAAcagcagca                                                                                                          <  2:8539/151‑1 (MQ=255)                                                    cgcaaaaccccccgcccgccAG‑CGAAAAACACACCGCGGTCCCCGGCGCCACCCACAGCACCGGTTGGCCCAGCACTTCCGGCATCGGGCA‑ATTTACCCCACCGACGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGca                                                                                                 <  1:745283/135‑1 (MQ=255)                                                        caATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAAtt                                                                                            >  1:161328/1‑151 (MQ=255)                                                         aaacccccctcggccGG‑CGAAAGACGAAACGGGGTCCACCGCCGGTGCCACAGCTCCGGTGGGGCCGGCAGTGCCGGGAACTGGCG‑ATTGACCCCGCCGACGTTCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTa                                                                                           <  1:274074/139‑1 (MQ=255)                                                              cccTGCCGCCAG‑CGCAATACGCACCGAGGCCCCCGGCGCCGGCCACAGCCCCGGTTGGGCCAGCACTTCCGGCAACGGGCG‑TTTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAaca                                                                                        <  2:435441/148‑1 (MQ=255)                                                              acCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACAcc                                                                                      >  2:439277/1‑151 (MQ=255)                                                                   ccgccAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTc                                                                                 >  1:965570/1‑151 (MQ=255)                                                                    ccccAG‑CGCAATCCGCAACGAGGCCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCCCTTCCGGCAACTGGCG‑ATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCg                                                                                <  2:933350/149‑1 (MQ=255)                                                                      ccAG‑CGCAATCCGCAACGAGGCCCACAGCCCCTGCCACAGCCCCGGTGGGGCCAGCACTTCCGGCAACGGGCG‑ATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCa                                                                              <  2:688243/151‑1 (MQ=255)                                                                           cgaaaTACGCAAAGAGGCCCACAGCGCCTGCCACAGCCCCGGGTGTGCCAGCCCTCCCGGAAACGGGAA‑ATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAAt                                                                           <  1:758699/147‑1 (MQ=255)                                                                             cAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCg                                                                        >  1:244778/1‑151 (MQ=255)                                                                              aaTCCGCAAGGAGGCCCACGGCGCCTGCCACAGCACGGGTTGGGCCAGCACTTCCGGCAACGGGCG‑ATTTACCCCAGCGAGGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCaaa                                                                            <  2:1010409/146‑1 (MQ=255)                                                                              aaTACGCAACGAGGTCCACGGCGCCTGCCACAGCACCGGTTGGGCCAGCCCTCCCGGCAACTGGCG‑ATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCg                                                                        <  2:734503/150‑1 (MQ=255)                                                                              aaTACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACGGGCG‑ATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGc                                                                         <  2:847574/149‑1 (MQ=255)                                                                                     aaCGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGc                                                                 >  2:276787/1‑150 (MQ=255)                                                                                      aCGAGGCCCACGGCGCCTGCCACAGCACCGGTTGTGCCAGCACTCCCGGCAACTGGCG‑TTTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAg                                                               <  2:293262/151‑1 (MQ=255)                                                                                       cGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGc                                                                 >  2:499990/1‑148 (MQ=255)                                                                                          ggTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACg                                                            >  2:398628/1‑150 (MQ=255)                                                                                            cccACAGCGCCTGCCACAGCACCGGTTGTGCCAGCCCTTCCGGCAAGTGGCG‑ATTTCCCCAACCGAAGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATc                                                         <  1:224652/150‑1 (MQ=255)                                                                                             ccccaGCCCCTCCCCCACCCCCGGTTGTGCCAGCCCTCCCGGCACCGGGCG‑ATTTCCCCCATCGCCGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCg                                                        <  1:675770/148‑1 (MQ=255)                                                                                             ccACAGCGCCTGCCACAGCACCGGTTGTGCCAGCCCTTCCGGCAACTGGCG‑TTTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCg                                                        <  2:1000783/151‑1 (MQ=255)                                                                                             ccACACCGCCTGCCACAGCAGCGGTTGTGCCAGCACTCCCGGCAGGGGGCG‑ATTTCCCCGACGGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGAt                                                          <  2:824830/149‑1 (MQ=255)                                                                                              cacaGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGt                                                       >  1:458849/1‑151 (MQ=255)                                                                                                    gcCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGt                                                 >  2:33984/1‑151 (MQ=255)                                                                                                       tGCCACAGCACGGGTTGGCCCAGCACTCCCGGCAATGGGCG‑ATTTCCCCCACCGCCGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGt                                                       <  2:462841/142‑1 (MQ=255)                                                                                                         ccACAGCACCGGTTGTGCCAGCCCTCCCGGAAACTGGCG‑ATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTcgcg                                             <  2:305452/150‑1 (MQ=255)                                                                                                                 ccGGTTGGGCCAGCACTTCCGGAAACTGGCG‑ATTTCCCCCACCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTg                                    <  2:432013/151‑1 (MQ=255)                                                                                                                     ttGGGCCGGCCCTCCCGGCACCGGGCG‑TTTTCCCCCAACGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCa                                          <  1:226983/141‑1 (MQ=255)                                                                                                                      tgtgCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCt                                      >  2:829340/1‑144 (MQ=255)                                                                                                                      tgtgCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTgcagc                                >  1:962463/1‑150 (MQ=255)                                                                                                                              cACTCCCGTCAACTGGCG‑ATTCCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCgtggt                        <  1:404219/150‑1 (MQ=255)                                                                                                                                cTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGcc                     >  1:148637/1‑151 (MQ=255)                                                                                                                                 ttCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCg                    >  2:739100/1‑151 (MQ=255)                                                                                                                                    cGGCACCGGGCG‑ATTTCCCCCACCGACGACCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCggg                  <  1:890978/150‑1 (MQ=255)                                                                                                                                            ggCT‑ATTTCCCCCACCGACGCCCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATg           <  1:394755/149‑1 (MQ=255)                                                                                                                                            ggCG‑ATTTCCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAAt            <  2:438329/148‑1 (MQ=255)                                                                                                                                              cG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCt       >  2:347758/1‑151 (MQ=255)                                                                                                                                               g‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCtt      >  1:709164/1‑151 (MQ=255)                                                                                                                                                 aTTTACCCCATCGCCCATCACCGCCAGTAACGACGGCAGCAACAGCAGCAGCGCCAAAACAATTAAGACCGTGTCGCAAATGCGGCTATGAAGCCGATCATCCGGGAAGCGCCAACCGTTCAGCAGCGTAGTGCCCGgcgataggacc        >  1:110815/1‑140 (MQ=255)                                                                                                                                                 aTTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCtt      >  1:1025290/1‑150 (MQ=255)                                                                                                                                                     aCCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCTTACTc  >  2:936924/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                      GCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGTCAGCACTACGCACAATACACCTGCCGCCAG‑CGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACCGGTTGTGCCAGCACTTCCGGCAACTGGCG‑ATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCAACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCGCCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCTTACTC  >  NC_000913/73435‑73730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑