Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,362,600	+C	noncoding (27/76 nt)	pheU ←	tRNA‑Phe

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,362,596	1	.	C	98.1%	202.9 / ‑2.5	53	noncoding (31/76 nt)	pheU	tRNA‑Phe
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (30/22);  total (30/23)
Fisher's exact test for biased strand distribution p-value = 4.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

AGAATCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAAT‑CCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTCTGTCAGG  >  NC_000913/4362447‑4362737                                                                                                                                                       |                                                                                                                                              agaATCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAAT‑c                                                                                                                                              >  2:45184/1‑151 (MQ=255)       tGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAAT‑ccccctg                                                                                                                                        >  2:852046/1‑148 (MQ=255)        ggTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAAT‑ccccct                                                                                                                                         <  2:730385/149‑3 (MQ=255)            gAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGctct                                                                                                                                     >  2:170033/1‑150 (MQ=255)             aGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTAc                                                                                                                                   >  2:829156/1‑151 (MQ=255)                   gTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTg                                                                                                                             >  1:842943/1‑151 (MQ=255)                            aTTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATc                                                                                                                      >  1:533521/1‑149 (MQ=255)                            aTTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCg                                                                                                                    <  2:881337/151‑1 (MQ=255)                                  aGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAAc                                                                                                              >  2:313664/1‑151 (MQ=255)                                     cAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACggg                                                                                                           >  1:467443/1‑151 (MQ=255)                                     cAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGGTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACggg                                                                                                           >  2:79533/1‑151 (MQ=255)                                       gAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGgc                                                                                                         <  1:874827/151‑1 (MQ=255)                                       gAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGgc                                                                                                         <  1:830635/151‑1 (MQ=255)                                               aaaTCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTaaa                                                                                                 <  2:469148/151‑1 (MQ=255)                                               aaaTCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTaa                                                                                                  >  1:138183/1‑150 (MQ=255)                                               aaaTCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTaa                                                                                                  >  2:445182/1‑150 (MQ=255)                                                 aTCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAAcc                                                                                               <  2:301829/151‑1 (MQ=255)                                                   cGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCg                                                                                              <  2:180679/150‑1 (MQ=255)                                                   cGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGt                                                                                             <  2:938940/151‑1 (MQ=255)                                                    gTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGt                                                                                             >  1:296986/1‑150 (MQ=255)                                                    gTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTa                                                                                            <  1:689944/151‑1 (MQ=255)                                                    gTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTa                                                                                            <  1:384166/151‑1 (MQ=255)                                                       gCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATc                                                                                         <  1:717569/151‑1 (MQ=255)                                                              gAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACAt                                                                                  >  2:777760/1‑151 (MQ=255)                                                                        aCGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCCTTAAACCGTAATCTGCACATCTCGTCAAcc                                                                        >  2:791511/1‑151 (MQ=255)                                                                        aCGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAAcc                                                                        >  1:176254/1‑151 (MQ=255)                                                                          ggACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTa                                                                      <  1:880924/151‑1 (MQ=255)                                                                          ggACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTa                                                                      <  2:397436/151‑1 (MQ=255)                                                                           gACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTaa                                                                     <  2:947805/151‑1 (MQ=255)                                                                            aCCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAAt                                                                    >  2:738682/1‑151 (MQ=255)                                                                              cTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAAttt                                                                  >  2:697074/1‑151 (MQ=255)                                                                              cTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAAttt                                                                  >  1:870279/1‑151 (MQ=255)                                                                                ccGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTc                                                                 <  1:153116/150‑1 (MQ=255)                                                                                       ggTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTaaa                                                           >  2:239347/1‑149 (MQ=255)                                                                                        gTCCGTTTATATGAATTTGGTGTCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAg                                                         <  2:627095/150‑1 (MQ=255)                                                                                            gTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGAtt                                                    >  2:912715/1‑151 (MQ=255)                                                                                              ttATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTc                                                   >  2:387103/1‑150 (MQ=255)                                                                                                    gAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCt                                            >  2:712036/1‑151 (MQ=255)                                                                                                      aTTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCtt                                           >  2:628242/1‑150 (MQ=255)                                                                                                      aTTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTa                                          <  2:845035/151‑1 (MQ=255)                                                                                                                 ggACTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGc                                >  2:726602/1‑150 (MQ=255)                                                                                                                    cTCGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAAt                            >  2:820262/1‑151 (MQ=255)                                                                                                                      cGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATc                           <  2:542050/150‑1 (MQ=255)                                                                                                                      cGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCg                          >  1:23855/1‑151 (MQ=255)                                                                                                                      cGGAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCg                          <  1:230065/151‑1 (MQ=255)                                                                                                                       ggAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGc                         >  1:8185/1‑151 (MQ=255)                                                                                                                       ggAATCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGc                         <  1:165696/151‑1 (MQ=255)                                                                                                                         aaTCGAACCAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGctt                       >  2:941461/1‑151 (MQ=255)                                                                                                                            cGAACCAAGGACACGGGGATTTTCAAT‑CCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCttt                   <  1:611736/151‑1 (MQ=255)                                                                                                                                ccAAGGACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCt                >  2:322078/1‑151 (MQ=255)                                                                                                                                     gACACGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGtt           <  1:458637/151‑1 (MQ=255)                                                                                                                                      acacGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGttt          >  2:950460/1‑151 (MQ=255)                                                                                                                                       cacGGGGATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTc         >  2:526897/1‑151 (MQ=255)                                                                                                                                             gATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTCTGTc     >  1:804169/1‑149 (MQ=255)                                                                                                                                             gATTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTCTGTCAg   <  1:829072/151‑1 (MQ=255)                                                                                                                                              aTTTTCAATCCCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTCTGTCAgg  <  1:45184/151‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                              AGAATCTGGTTGAGTTCGGTAGAATTGATTTGGAGGCAGAACGCTTAAATCGTGGCGTCCTGAAACGAAAAACGGACCTCCGTGGAGGTCCGTTTATATGAATTTGGTGCCCGGACTCGGAATCGAACCAAGGACACGGGGATTTTCAAT‑CCCCTGCTCTACCGACTGAGCTATCCGGGCAACGGGGCGCATTAAACCGTAATCTGCACATCTCGTCAACCTAATTTCAGTAAAAGCGATTCAACTGCTTAAGATTGCGGCAAATCGCTTCTTTTCTGTGTTTCTGTCAGG  >  NC_000913/4362447‑4362737

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑