Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,986,686	C→T	*399* (TAG→TAA)	hemY ←	putative protoheme IX synthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,986,686	0	C	T	98.4%	203.3 / ‑4.3	65	*399* (TAG→TAA)	hemY	putative protoheme IX synthesis protein
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (34/29);  total (34/31)
Fisher's exact test for biased strand distribution p-value = 4.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.07e-01

GTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGCGTAATCGTAG  >  NC_000913/3986563‑3986800                                                                                                                            |                                                                                                                   gTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTa                                                                                                     <  2:988227/139‑1 (MQ=255)    gAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTc                                                                                                  >  1:1728532/1‑139 (MQ=255)     aGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCt                                                                                                 <  2:900743/139‑1 (MQ=255)     aGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCt                                                                                                 <  2:1461411/139‑1 (MQ=255)          aGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAAc                                                                                            >  1:516566/1‑139 (MQ=255)                             aCAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcgc                                                                         >  2:1314415/1‑139 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        >  2:392861/1‑105 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        >  2:381502/1‑105 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        <  1:392861/105‑1 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        <  1:381502/105‑1 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGAc                                                                      >  1:1462023/1‑139 (MQ=255)                                gACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGAc                                                                      >  1:1866964/1‑139 (MQ=255)                                   cTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCa                                                                   >  2:735186/1‑139 (MQ=255)                                   cTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCa                                                                   >  1:1603214/1‑139 (MQ=255)                                   cTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCa                                                                   <  2:1868214/139‑1 (MQ=255)                                    tGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCAt                                                                  <  2:1462023/139‑1 (MQ=255)                                        ttAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGTCGCATAGCt                                                              <  2:516566/139‑1 (MQ=255)                                             gCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGc                                                         <  2:1728532/139‑1 (MQ=255)                                                        aataaGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCt                                              <  1:364137/139‑1 (MQ=255)                                                           aaGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTtgt                                           <  2:1866964/139‑1 (MQ=255)                                                            agagCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGc                                                                                                           >  1:165074/1‑74 (MQ=255)                                                            agagCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGc                                                                                                           <  2:165074/74‑1 (MQ=255)                                                               gCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAattact                                                                                                                <  2:1585537/66‑1 (MQ=255)                                                               gCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAattact                                                                                                                >  1:1585537/1‑66 (MQ=255)                                                               gCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcg                                                                          <  2:878985/104‑1 (MQ=255)                                                               gCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcg                                                                          >  1:878985/1‑104 (MQ=255)                                                                 aGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGc                                                                    >  1:608406/1‑108 (MQ=255)                                                                 aGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGc                                                                    <  2:608406/108‑1 (MQ=255)                                                                  ggCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        >  1:429590/1‑71 (MQ=255)                                                                  ggCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        <  2:429590/71‑1 (MQ=255)                                                                  ggCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCt                                    >  1:26102/1‑139 (MQ=255)                                                                   gCGTTTTTTTATGTAGCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTg                                   >  1:1254187/1‑139 (MQ=255)                                                                    cGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGtt                                                                                         <  1:1538697/84‑1 (MQ=255)                                                                    cGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGtt                                                                                         >  2:1538697/1‑84 (MQ=255)                                                                      tttttttATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGtt                                                                                         <  1:699621/82‑1 (MQ=255)                                                                      tttttttATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGtt                                                                                         >  2:699621/1‑82 (MQ=255)                                                                        tttttATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAg                              >  1:1204763/1‑139 (MQ=255)                                                                                 aTCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCa                                        >  2:1348309/1‑120 (MQ=255)                                                                                 aTCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAAGTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCa                                        <  1:1348309/120‑1 (MQ=255)                                                                                   cAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        >  1:1761111/1‑54 (MQ=255)                                                                                   cAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        <  2:1761111/54‑1 (MQ=255)                                                                                   cAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTg                                                             <  2:1630404/97‑1 (MQ=255)                                                                                   cAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTg                                                             >  1:1630404/1‑97 (MQ=255)                                                                                   cAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCaa                   >  1:1595699/1‑139 (MQ=255)                                                                                         ggCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACtgtg                                                                                                             >  1:399895/1‑43 (MQ=255)                                                                                         ggCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACtgtg                                                                                                             <  2:399895/43‑1 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        <  1:464493/47‑1 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCggg                                                                                                        >  2:464493/1‑47 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCaaa                                                                                >  2:16354/1‑71 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCaaa                                                                                <  1:16354/71‑1 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGc            <  2:1595699/139‑1 (MQ=255)                                                                                          gCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGc            >  1:650614/1‑139 (MQ=255)                                                                                           ccccGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCt                                                                                                 <  1:1018619/53‑1 (MQ=255)                                                                                           ccccGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCt                                                                                                 >  2:1018619/1‑53 (MQ=255)                                                                                           ccccGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGc                                                         <  2:713153/93‑1 (MQ=255)                                                                                           ccccGGAGGTGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGc                                                         >  1:713153/1‑93 (MQ=255)                                                                                                    tGCTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGCGTAATCGTAg  >  1:1053893/1‑139 (MQ=255)                                                                                                      cTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGCGTAATCGTAg  <  2:74407/137‑1 (MQ=255)                                                                                                      cTTGCCTCCGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGCGTAATCGTAg  >  1:74407/1‑137 (MQ=255)                                                                                                             ccGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcg                                                                          <  1:1202754/58‑1 (MQ=255)                                                                                                             ccGGGTGAGAAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTcg                                                                          >  2:1202754/1‑58 (MQ=255)                                                                                                                ggTGAGAAGGAATTACTGTGGCGGGTTATTCTGCa                                                                                              >  1:1331309/1‑35 (MQ=255)                                                                                                                ggTGAGAAGGAATTACTGTGGCGGGTTATTCTGCa                                                                                              <  2:1331309/35‑1 (MQ=255)                                                                                                                    agaAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGc            >  1:375388/1‑113 (MQ=255)                                                                                                                    agaAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGc            <  2:375388/113‑1 (MQ=255)                                                                                                                     gaAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGa                                                                       <  2:1848185/53‑1 (MQ=255)                                                                                                                     gaAGGAATTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGa                                                                       >  1:1848185/1‑53 (MQ=255)                                                                                                                            |                                                                                                                   GTTGAGTGAAGCACCCACTTGTTGTCATACAGACCTGTTTTAACGCCTGCTCCGTAATAAGAGCAGGCGTTTTTTTATGTATCAGGAAGGCCCCGGAGGTGCTTGCCTCCGGGTGAGAAGGAACTACTGTGGCGGGTTATTCTGCAACGTTAACATCAAACCGTCGCGACGCATAGCTGCAGCTTCTTCCGGCTTGTGCAGTCTGTCCAGCGCGTCGGCAAGCCATGCGTAATCGTAG  >  NC_000913/3986563‑3986800

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑