Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,937,409	C→T	A39V (GCA→GTA)	rbsK →	ribokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,937,409	0	C	T	98.2%	182.5 / ‑4.2	56	A39V (GCA→GTA)	rbsK	ribokinase
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (23/31);  total (25/31)
Fisher's exact test for biased strand distribution p-value = 4.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

TTTATGGACATCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGCATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACATTGATA  >  NC_000913/3937276‑3937543                                                                                                                                      |                                                                                                                                       tttATGGACATCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTgg                                                                                                                                  <  2:169750/140‑1 (MQ=255)           tCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTAt                                                                                                                                      >  1:633888/1‑126 (MQ=255)           tCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGgc                                                                                                                        >  1:105928/1‑140 (MQ=255)           tCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGgc                                                                                                                        <  2:15633/140‑1 (MQ=255)           tCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGGAGCCACTATCAGGTTAAATTTGGCCGCAAAGgc                                                                                                                        >  2:344248/1‑140 (MQ=255)                 atatGCAAAACGCAGGCCGCCTCGTTGTTCTTGGCTGCATTAATGCTGCCCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAAt                                                                                                                  <  2:232034/140‑1 (MQ=255)                    tGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAg                                                                                                               <  1:61513/140‑1 (MQ=255)                    tGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAg                                                                                                               <  1:474020/140‑1 (MQ=255)                    tGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAg                                                                                                               >  1:138144/1‑140 (MQ=255)                           cGCAGGCAGCCTCGTAGTTCTTAGCTGCAATAATGCTTACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTgg                                                                                                        <  1:344248/140‑1 (MQ=255)                              aggcagCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTGGTATTTGCCGGGAAGGGCGCGGATCAGGCTGTGgctg                                                                                                     >  1:278535/1‑140 (MQ=255)                                gcagCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGgctgct                                                                                                   <  1:177258/140‑1 (MQ=255)                                     cTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCg                                                                                              >  1:619952/1‑140 (MQ=255)                                                  gcagcaTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAat                                                                                 >  2:164517/1‑140 (MQ=255)                                                    agcaTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGTATCAGGCGGTGGCTACTGGGCATAGCGGTGCGAatat                                                                               >  1:196495/1‑140 (MQ=255)                                                      caTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATcg                                                                             <  1:413375/140‑1 (MQ=255)                                                      caTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATcg                                                                             >  2:607617/1‑140 (MQ=255)                                                      caTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATcg                                                                             >  2:97726/1‑140 (MQ=255)                                                      caTTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGCCGTAGCGGTGCCAATATcg                                                                             <  2:423046/140‑1 (MQ=255)                                                           aTGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGttt                                                                        <  1:367605/140‑1 (MQ=255)                                                           aTGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGttt                                                                        <  1:99686/140‑1 (MQ=255)                                                              cTGACCACATTCTTAATTTTCAATCTTTTCCTACTCCAGTCGAAACCGGAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTAtt                                                                     <  2:278535/140‑1 (MQ=255)                                                              cTGACCACATTCTTAATCTTCAGTCGTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTAtt                                                                     <  1:264239/140‑1 (MQ=255)                                                                     caTTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTa                                                              <  1:670238/140‑1 (MQ=255)                                                                     caTTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTa                                                              <  2:105928/140‑1 (MQ=255)                                                                     caTTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTa                                                              <  2:138144/140‑1 (MQ=255)                                                                      aTTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTa                                                                       >  1:394967/1‑130 (MQ=255)                                                                      aTTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTa                                                                       <  2:394967/130‑1 (MQ=255)                                                                            aaTCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGtga                                                       >  1:526679/1‑140 (MQ=255)                                                                                ttCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGAc                                                   >  2:573420/1‑140 (MQ=255)                                                                                ttCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGCATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGGGGTGCGACTATCGCGTCTATTTACTGTACGCGTGATGAc                                                   >  2:343139/1‑140 (MQ=255)                                                                                 tCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCACGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACa                                                  <  1:693991/140‑1 (MQ=255)                                                                                   aaTCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGc                                                <  1:164517/140‑1 (MQ=255)                                                                                               cTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGc                                    >  2:161498/1‑140 (MQ=255)                                                                                                 ccAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTTATGACAACATTGGTGAGAGCGt                                  >  1:318725/1‑140 (MQ=255)                                                                                                   aGGCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTc                                >  1:110315/1‑140 (MQ=255)                                                                                                    ggCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCg                               >  2:429175/1‑140 (MQ=255)                                                                                                    ggCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCg                               >  1:375523/1‑140 (MQ=255)                                                                                                     gCGAAACCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGc                              >  2:141678/1‑140 (MQ=255)                                                                                                         aaCCGTAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCcagc                          >  1:571048/1‑140 (MQ=255)                                                                                                              tAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTTGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTc                     >  1:712734/1‑140 (MQ=255)                                                                                                              tAACCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTc                     >  1:391423/1‑140 (MQ=255)                                                                                                                aCCGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGc                   <  1:573420/140‑1 (MQ=255)                                                                                                                 ccGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGcc                  <  2:375523/140‑1 (MQ=255)                                                                                                                  cGGTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCa                 <  1:540536/140‑1 (MQ=255)                                                                                                                   ggTAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCAc                <  2:619952/140‑1 (MQ=255)                                                                                                                     tAACCACTATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTg              >  1:400143/1‑140 (MQ=255)                                                                                                                       aCCACTATCAGGTTGTATTTGGGGGCAAAGGCGCGGATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGAt            <  2:227708/140‑1 (MQ=255)                                                                                                                            tATCAGGTTGTATTTGTAGGCAAAGGCGCGAATCACGCTTTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAt       <  2:313633/140‑1 (MQ=255)                                                                                                                            tATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAt       <  1:141678/140‑1 (MQ=255)                                                                                                                            tATCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAt       <  1:97726/140‑1 (MQ=255)                                                                                                                             aTCAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAtt      <  2:137178/140‑1 (MQ=255)                                                                                                                               cAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGTTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAt       <  2:113436/137‑1 (MQ=255)                                                                                                                               cAGGTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGTTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACAt       >  1:113436/1‑137 (MQ=255)                                                                                                                                 ggTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACATTGata  <  1:38551/140‑1 (MQ=255)                                                                                                                                 ggTTGTATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACATTGata  <  1:589061/140‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       TTTATGGACATCCCGAATATGCAAAACGCAGGCAGCCTCGTTGTTCTTGGCAGCATTAATGCTGACCACATTCTTAATCTTCAATCTTTTCCTACTCCAGGCGAAACCGTAACCGGTAACCACTATCAGGTTGCATTTGGCGGCAAAGGCGCGAATCAGGCTGTGGCTGCTGGGCGTAGCGGTGCGAATATCGCGTTTATTGCCTGTACGGGTGATGACAGCATTGGTGAGAGCGTTCGCCAGCAGCTCGCCACTGATAACATTGATA  >  NC_000913/3937276‑3937543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑