Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,946,246	G→A	20.5%	noncoding (2543/2904 nt)	rrlC →	23S ribosomal RNA of rrnC operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,946,246	0	G	A	20.5%	110.7 / 21.9	64	noncoding (2543/2904 nt)	rrlC	23S ribosomal RNA of rrnC operon
Reads supporting (aligned to +/- strand):  ref base G (23/27);  new base A (3/10);  total (26/38)
Fisher's exact test for biased strand distribution p-value = 2.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.93e-01

GGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGG  >  NC_000913/3946147‑3946327                                                                                                    |                                                                                  ggggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAg                                                                                   <  1:990940/100‑1 (MQ=33) ggggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAg                                                                                   <  1:1080880/100‑1 (MQ=33) ggggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCAAAg                                                                                   <  2:117032/100‑1 (MQ=17)  gggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAgg                                                                                  <  1:1947522/100‑1 (MQ=33)   ggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAggg                                                                                 <  1:1150919/100‑1 (MQ=33)   ggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAggg                                                                                 <  1:1450221/100‑1 (MQ=32)   ggATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAggg                                                                                 <  1:2049307/100‑1 (MQ=33)       aaCAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATg                                                                             <  1:628738/100‑1 (MQ=33)       aaCAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGAACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATg                                                                             <  1:210847/100‑1 (MQ=18)        agaGGCTGATACCACCCAAGAGTTCATATCGACGGCGGTGTTAGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATgg                                                                            >  1:1734372/3‑100 (MQ=255)        aCAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATgg                                                                            >  1:1065859/1‑100 (MQ=32)         cAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGc                                                                           <  2:1773006/100‑1 (MQ=33)         cAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGc                                                                           <  2:209108/100‑1 (MQ=18)           ggCTGATACCGCCCAAGCGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCCCATCCAGGAGCTGACGTAGGTCCCAAGGGCATGGCTg                                                                         >  2:1725342/1‑100 (MQ=11)             cTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGtt                                                                       >  1:2264490/1‑100 (MQ=32)               gATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCg                                                                     <  2:1261078/100‑1 (MQ=18)                   ccGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCAt                                                                 <  2:2065723/100‑1 (MQ=18)                    cGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCAtt                                                                >  1:259507/1‑100 (MQ=32)                      cccAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTa                                                              >  1:165087/1‑100 (MQ=32)                      cccAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTa                                                              <  1:1079606/100‑1 (MQ=33)                      cccAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTa                                                              >  1:1778074/1‑100 (MQ=17)                         aaGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAg                                                           <  2:2478597/100‑1 (MQ=18)                         aaGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAg                                                           <  2:179462/100‑1 (MQ=17)                          agagTTCATCTCGCCGGCGGTGTTTGGCACATCGATGTAGGCTCCTTACCTCCTGGAGATGACGTCGGTCCCCACGGTATGGCTGTTCGCAATTTGAAg                                                           <  2:2137361/99‑1 (MQ=2)                          agagTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGTAGTAGGTCCCAAGGGTATGGCTGTTGGCCATTTAAAGt                                                          >  2:890217/1‑100 (MQ=12)                           gagTTCATATCGACGGCGGTGTTTGGTACCTCGATGTCGGTTCATCACATCCAGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAGTg                                                         <  2:260267/100‑1 (MQ=11)                            agTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTgg                                                        <  2:1930050/100‑1 (MQ=33)                            agTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAGTg                                                         <  2:2048431/99‑1 (MQ=17)                             gTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTGGCCATTTAAAGTGGt                                                       >  2:1211440/1‑100 (MQ=17)                              ttCGTATCGACGGCGGTGTTTGGCACCTCGCTGTAGTCTTATCAAATCCTATAGCTGAAGTAAGTCCCAAATTTATTACTGTTCTCCATTTAAAg                                                           <  2:2393713/95‑1 (MQ=2)                                cATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTAcg                                                    <  2:945537/100‑1 (MQ=32)                                cATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTAcg                                                    >  1:2000158/1‑100 (MQ=33)                                    tCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAg                                                <  2:178046/100‑1 (MQ=33)                                     cGACGGCGGTGTTTGGCACCTCGATGTCGGATCATCACATCCTGAAGCTGAAATAGGTCCCAAAGGTATGGATGTTCGCCATTTAAAGTGGTACGCGa                                                 >  2:1453665/1‑98 (MQ=11)                                      gACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCt                                              >  1:1770588/1‑100 (MQ=33)                                        cggcggTGTTTGGCACCTCGATGTCGTCTCATCACATCCTGGAGCTGAAGTAGTTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTAcg                                                    >  2:1986064/1‑92 (MQ=12)                                          gcggTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGt                                          >  1:1767233/1‑100 (MQ=33)                                           cggTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGtt                                         <  1:2371909/100‑1 (MQ=32)                                           cggTGTTTGGCACATCGATGTAGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGtt                                         >  2:2546528/1‑100 (MQ=12)                                            ggTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGttt                                        <  2:2528417/100‑1 (MQ=33)                                            ggTGTTGGGTACCTCGTTGTCGGCTCATCACATCCTGGAGCTGAAGTGGGTCCCAAGGGTATGGCTGTTCGCCTTTTAAAGTGGTACGCGAGCTGGGttt                                        <  2:1620853/100‑1 (MQ=11)                                             gtgtTTGGCACCTCGATGTCGGCTCAGCACATCCTGGAGCTGAAGTAGGTACCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTa                                       <  2:1728832/100‑1 (MQ=12)                                               gtTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAg                                      >  1:1649960/1‑99 (MQ=32)                                               gtTTGGCACCTCGATGTCCGATCATCACATCCTGTAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATGTAAAGTGGTACGCGAGCTGGGTTTAGa                                     <  2:1756771/100‑1 (MQ=11)                                                 ttGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAc                                   <  1:1924075/100‑1 (MQ=33)                                                 ttGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAc                                   >  1:115267/1‑100 (MQ=32)                                                     naCCTCAATGTCGACTCATCACATACGGAATCTGAAGTAGGTCCCAAGGGTATTGTTGTTCGCCATATAAAGTGGTACGCGAACGGGCTTTAGAAcatc                                >  2:1124309/2‑99 (MQ=2)                                                     cACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAcgtcg                               <  1:1619354/100‑1 (MQ=32)                                                     cACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAcgtcg                               <  1:1991324/100‑1 (MQ=33)                                                     cACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAcgtcg                               >  2:306959/1‑100 (MQ=32)                                                     cACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAAcgtcg                               <  2:1778061/100‑1 (MQ=17)                                                        cTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTga                            <  2:1792072/100‑1 (MQ=32)                                                         tCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTgag                           <  1:1124983/100‑1 (MQ=33)                                                         tCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTgag                           <  2:2438977/100‑1 (MQ=33)                                                          cGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTgaga                          >  1:1056181/1‑100 (MQ=32)                                                           gATGTCGGCGCATCACATCCTGGAGCTGAAGTCGGTCCCAAGGGTGTGGCTGGTCGCCATTTAAAGTCGTACGGGAGCTAGGGTTAGAACGTCGTGAGAc                         <  2:1573326/100‑1 (MQ=11)                                                             tGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAg                       >  1:785375/1‑100 (MQ=33)                                                             tGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAg                       <  2:259504/100‑1 (MQ=33)                                                              gTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGt                      >  1:90238/1‑100 (MQ=18)                                                               tCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGtt                     <  2:2174816/100‑1 (MQ=32)                                                                cGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTc                    <  1:594708/100‑1 (MQ=32)                                                                  gCTCATCACATCCTGGAGCTGAAGTAGGGCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCg                   <  2:1144943/99‑1 (MQ=17)                                                                      atcaCATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTccc              <  1:972358/100‑1 (MQ=33)                                                                       tcaCATCCTGGAGCTAAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCt             >  2:1140001/1‑100 (MQ=17)                                                                          caTCCTGGAGCTGAAGTAGGTCCCAAAGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATc          <  2:1515661/100‑1 (MQ=18)                                                                             ccTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGc       <  1:2211014/100‑1 (MQ=33)                                                                             ccTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGc       <  2:332371/100‑1 (MQ=33)                                                                               tGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCg     >  2:436004/1‑100 (MQ=32)                                                                                 gAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTg   <  2:2093572/100‑1 (MQ=31)                                                                                  aGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTgg  >  2:682177/1‑100 (MQ=11)                                                                                  aGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTgg  >  1:474870/1‑100 (MQ=11)                                                                                                    |                                                                                  GGGGATAACAGGCTGATACCGCCCAAGAGTTCATATCGACGGCGGTGTTTGGCACCTCGATGTCGGCTCATCACATCCTGGAGCTGAAGTAGGTCCCAAGGGTATGGCTGTTCGCCATTTAAAGTGGTACGCGAGCTGGGTTTAGAACGTCGTGAGACAGTTCGGTCCCTATCTGCCGTGG  >  NC_000913/3946147‑3946327

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: ‑