Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,182,712	G→A	A55T (GCC→ACC)	zupT →	zinc transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,182,712	0	G	A	94.9%	178.7 / ‑1.1	59	A55T (GCC→ACC)	zupT	zinc transporter
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base A (20/36);  total (22/37)
Fisher's exact test for biased strand distribution p-value = 5.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.24e-01

CGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTGCCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTGCC  >  NC_000913/3182615‑3182806                                                                                                   |                                                                                               cGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTAcc                                                                                              <  1:36823/100‑1 (MQ=255)   ttCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGc                                                                                            <  2:590330/100‑1 (MQ=255)    tctcGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCa                                                                                           <  1:1565221/100‑1 (MQ=255)       cGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTa                                                                                        <  2:1147324/100‑1 (MQ=255)       cGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTa                                                                                        <  1:31103/100‑1 (MQ=255)         ggCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTagc                                                                                      >  1:962820/1‑100 (MQ=255)          gCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGTGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTagca                                                                                     <  1:743527/100‑1 (MQ=255)          gCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTagca                                                                                     <  2:1012324/100‑1 (MQ=255)            aaaaaCCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTagcagc                                                                                   >  2:1623450/1‑100 (MQ=255)             aaaaCCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGTATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCt                                                                                  >  1:1219149/1‑100 (MQ=255)               aaCCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGa                                                                                <  1:463210/100‑1 (MQ=255)                 cccTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAg                                                                              >  2:1621029/1‑100 (MQ=255)                   cTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGa                                                                            >  2:667849/1‑100 (MQ=255)                      gAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATg                                                                         <  2:96093/100‑1 (MQ=255)                           gCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGcc                                                                    <  2:252746/100‑1 (MQ=255)                              tACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCtn                                                                  <  2:712277/99‑2 (MQ=255)                                cTGGCGTTTTCGCTATGTTTTGCGGCGGAGATCATGTTGCTCGTCTC‑CTTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTgtgt                                                               <  1:278986/100‑1 (MQ=255)                                   gCGTTTTCTCTAGGTTTTGCGGCGGGGATCATGTGGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTgg                                                            <  2:1219160/100‑1 (MQ=255)                                     gTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGt                                                          <  2:974665/100‑1 (MQ=255)                                     gTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGt                                                          <  1:1628079/100‑1 (MQ=255)                                     gTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGt                                                          <  2:65739/100‑1 (MQ=255)                                          cGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATTTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCCGAAGGAATGTCGCCTGTGTTGGGCTAt                                                       >  1:142715/1‑98 (MQ=255)                                                 ttttGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGttt                                              <  2:1639251/100‑1 (MQ=255)                                                  tttGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTa                                             >  2:758219/1‑100 (MQ=255)                                                    tGCGGTGGGTATTTTGTTTTTCATTTT‑TTTAATGGAAATGCTTTCTACCGGACTAGCAGCTGAAGGAATGGCGCCTGTGTTGGGTTATGGAATGTTTATc                                           <  2:282082/100‑1 (MQ=255)                                                    tGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATc                                           <  2:279265/100‑1 (MQ=255)                                                    tGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATc                                           <  2:1047822/100‑1 (MQ=255)                                                     gtggcggGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTGCCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCt                                          >  2:1227676/3‑100 (MQ=255)                                                       ggcggGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTc                                        >  2:1415357/1‑100 (MQ=255)                                                        gcggGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCg                                       <  1:758215/100‑1 (MQ=255)                                                         cggGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCgg                                      >  1:573052/1‑100 (MQ=255)                                                         cggGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCgg                                      <  1:783344/100‑1 (MQ=255)                                                              aTCATGTTGCTCATTTC‑ATTAATGGATATGTTTCCTACCGCAATAGGAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCt                                   <  2:142715/98‑1 (MQ=255)                                                               tCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCt                                <  1:1267616/100‑1 (MQ=255)                                                               tCATGGTGCTCA‑CTCTATTAATGGTAATGATGCCTGCGGCACTGGCAGCTGAAGGAATGTCGTCTTTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCt                                <  1:1759871/100‑1 (MQ=255)                                                                   gTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGTACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTgcc                            <  2:1232991/100‑3 (MQ=255)                                                                   gTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGc                            <  1:179593/100‑1 (MQ=255)                                                                   gTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGc                            <  2:859821/100‑1 (MQ=255)                                                                   gTTGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGc                            >  1:643785/1‑100 (MQ=255)                                                                   gTTGCTCATCTC‑ATTAATGGAAATGCTTACTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGc                            <  2:347222/100‑1 (MQ=255)                                                                     tGCTCATCTC‑ATTAATGGAAATGCTTCCTACCGCACTCGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTa                          >  1:971438/1‑100 (MQ=255)                                                                        tcatctc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTAttt                       >  1:402295/1‑100 (MQ=255)                                                                          atctc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTg                     >  2:568146/1‑100 (MQ=255)                                                                           tctc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTgg                    >  1:439834/1‑100 (MQ=255)                                                                           tctc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTgg                    >  1:421130/1‑100 (MQ=255)                                                                            ctc‑atTAATGGAAATGCTTCCTACCGCAATAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGc                   <  1:54829/100‑1 (MQ=255)                                                                             tc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGcc                  <  1:1179693/100‑1 (MQ=255)                                                                             tc‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGcc                  <  1:906191/100‑1 (MQ=255)                                                                              c‑atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCt                 >  1:1258224/1‑100 (MQ=255)                                                                                atTAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTg                >  1:1326381/1‑100 (MQ=255)                                                                                  tAATGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGa              >  1:1295470/1‑100 (MQ=255)                                                                                   aaTGGAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGAc             >  2:646073/1‑100 (MQ=255)                                                                                     tGGAAATGCTTCCTGCCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCg           >  1:1797814/1‑100 (MQ=255)                                                                                       gAAATGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCa         >  2:966943/1‑100 (MQ=255)                                                                                           tGCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGtt     <  1:1621018/100‑1 (MQ=255)                                                                                            gCTTTCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTg    <  2:697821/100‑1 (MQ=255)                                                                                            gCTTCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTg    <  1:1465119/100‑1 (MQ=255)                                                                                              ttCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTGcc  <  1:425787/100‑1 (MQ=255)                                                                                              ttCCTACCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTGcc  <  1:974353/100‑1 (MQ=255)                                                                                                   |                                                                                               CGTTCTCGGGCAAAAACCCTCGAACCGCTTACTGGCGTTTTCGCTAGGTTTTGCGGCGGGGATCATGTTGCTCATCTC‑ATTAATGGAAATGCTTCCTGCCGCACTAGCAGCTGAAGGAATGTCGCCTGTGTTGGGTTATGGAATGTTTATCTTCGGTCTGCTTGGCTATTTTGGCCTGGACCGCATGTTGCC  >  NC_000913/3182615‑3182806

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑