Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,193,289	T→A	Q162L (CAG→CTG)	mnmA ←	tRNA(Gln,Lys,Glu) U34 2‑thiouridylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,193,289	0	T	A	94.3%	231.9 / 5.1	70	Q162L (CAG→CTG)	mnmA	tRNA(Gln,Lys,Glu) U34 2‑thiouridylase
Reads supporting (aligned to +/- strand):  ref base T (2/2);  new base A (32/34);  total (34/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.42e-01

GTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGACGTA  >  NC_000913/1193192‑1193385                                                                                                  |                                                                                                 gTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGc                                                                                                >  1:729557/1‑100 (MQ=255)   cTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTc                                                                                              >  1:200449/1‑100 (MQ=255)    ttttttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGc                                                                                                <  2:1261357/97‑1 (MQ=255)       tttCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATgg                                                                                          <  1:660047/100‑1 (MQ=255)         tcttcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCt                                                                                        >  1:2031640/1‑100 (MQ=255)          cttcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTg                                                                                       >  2:727499/1‑100 (MQ=255)           ttcGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGATCATGGCTGa                                                                                      >  1:1181626/1‑100 (MQ=255)             cgcgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGc                                                                                    >  2:1390698/1‑100 (MQ=255)             cgcgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGc                                                                                    >  2:415194/1‑100 (MQ=255)              gcgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTAAGCg                                                                                   <  2:1400958/100‑1 (MQ=255)               cgGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGt                                                                                  <  2:1405540/100‑1 (MQ=255)                  tGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGTTTTGCGCAATCAGCTCATGGCTGAGCGtata                                                                               <  1:1374629/100‑1 (MQ=255)                  tGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGtat                                                                                <  1:1108676/99‑1 (MQ=255)                   gaccagaccaAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGtaaac                                                                              >  1:970631/1‑97 (MQ=255)                     ccagaccaAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAg                                                                            <  2:1066277/100‑1 (MQ=255)                     ccagaccaAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAg                                                                            >  2:1824626/1‑100 (MQ=255)                        gaccaAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGaa                                                                         <  1:539159/100‑1 (MQ=255)                           caAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTa                                                                      <  1:75279/100‑1 (MQ=255)                             aGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGc                                                                    <  1:1937717/100‑1 (MQ=255)                                tCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATATAGGAAGTAGctct                                                                 <  2:707834/100‑1 (MQ=255)                                tCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATATAGGAAGTAGctct                                                                 <  2:51357/100‑1 (MQ=255)                                tCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGctc                                                                  <  1:1922758/99‑1 (MQ=255)                                 cTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTg                                                                >  2:1436955/1‑100 (MQ=255)                                  ttCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTgg                                                               >  1:486292/1‑100 (MQ=255)                                  ttCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTgg                                                               <  1:415195/100‑1 (MQ=255)                                  ttCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTgg                                                               <  2:1511474/100‑1 (MQ=255)                                   tCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTACAAAGGAAGTAGCTCTgg                                                               >  1:587335/1‑99 (MQ=255)                                    cAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTc                                                             >  2:514275/1‑100 (MQ=255)                                    cAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTc                                                             <  1:17367/100‑1 (MQ=255)                                      gCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCtt                                                           >  2:1994707/1‑100 (MQ=255)                                      gCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCtt                                                           >  1:1543727/1‑100 (MQ=255)                                      gCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCtt                                                           >  1:1500713/1‑100 (MQ=255)                                       cAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCttt                                                          <  2:1515956/100‑1 (MQ=255)                                          tCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTAtt                                                       >  2:384941/1‑100 (MQ=255)                                               cGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGt                                                  <  1:102779/100‑1 (MQ=255)                                               cGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGt                                                  >  1:1767070/1‑100 (MQ=255)                                                 cACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTcc                                                <  1:753832/100‑1 (MQ=255)                                                 cACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTcc                                                <  1:1020978/100‑1 (MQ=255)                                                   ccgtcGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAAGCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAg                                              <  2:434432/96‑1 (MQ=255)                                                   ccTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAg                                              <  2:1020266/100‑1 (MQ=255)                                                   ccTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAg                                              >  1:1590487/1‑100 (MQ=255)                                                    cTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGa                                             >  1:262806/1‑100 (MQ=255)                                                     tGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGAc                                            >  1:448308/1‑100 (MQ=255)                                                        ggTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCAc                                         <  1:966335/100‑1 (MQ=255)                                                        ggTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCAc                                         <  1:1262993/100‑1 (MQ=255)                                                        ggTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCAc                                         >  1:207475/1‑100 (MQ=255)                                                         gTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACg                                        <  1:520356/100‑1 (MQ=255)                                                                cAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAgg                                 >  1:1161280/1‑100 (MQ=255)                                                                      gCCGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGctc                           <  2:978200/100‑1 (MQ=255)                                                                        cGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCtt                         >  1:245948/1‑100 (MQ=255)                                                                        cGACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCtt                         >  2:1527142/1‑100 (MQ=255)                                                                         gACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTACAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTg                        <  2:587333/100‑1 (MQ=255)                                                                         gACCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTAAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTg                        <  1:1436964/100‑1 (MQ=255)                                                                          aCCGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGc                       <  2:1158043/100‑1 (MQ=255)                                                                           ccGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGcc                      >  1:754668/1‑100 (MQ=255)                                                                           ccGGGAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGcc                      >  2:285197/1‑100 (MQ=255)                                                                             gggAACAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCAt                    >  1:593086/1‑100 (MQ=255)                                                                                 aCAGGCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGAc                <  1:741363/100‑1 (MQ=255)                                                                                    ggCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATc             >  1:2019956/1‑100 (MQ=255)                                                                                    ggCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATc             <  2:729555/100‑1 (MQ=255)                                                                                     gCTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCg            >  2:2032505/1‑100 (MQ=255)                                                                                      cTTTGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCgg           <  1:1768073/100‑1 (MQ=255)                                                                                       tttGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGc          <  2:2031622/100‑1 (MQ=255)                                                                                         tGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGccc        <  1:727501/100‑1 (MQ=255)                                                                                         tGCGCAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGccc        >  1:395179/1‑100 (MQ=255)                                                                                          gcgcAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGccca       <  2:262805/100‑2 (MQ=255)                                                                                          gcgcAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCg       <  2:1767056/100‑1 (MQ=255)                                                                                           cgcAATCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGa      >  2:843048/1‑100 (MQ=255)                                                                                               aTCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGacgta  >  2:2026236/1‑100 (MQ=255)                                                                                               aTCAGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGacgta  >  2:1978313/1‑100 (MQ=255)                                                                                                  |                                                                                                 GTCTTTTTTCTTCGCGGTGACCAGACCAAGATCTTCAGCAATCTTACGCACCTGCGGTTTTTCCAGTTCGCCGACCGGGAACAGGCTTTGCGCAATCTGCTCATGGCTGAGCGTATAAAGGAAGTAGCTCTGGTCTTTATTGCTGTCCAGACCACGCAGCAGGCGGCTCTTGCCATCGACATCGGCCCGACGTA  >  NC_000913/1193192‑1193385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑