Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,168,540	T→A	intergenic (+93/‑101)	gltT → / → rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,168,540	0	T	A	93.4%	189.1 / 4.9	76	intergenic (+93/‑101)	gltT/rrlB	tRNA‑Glu/23S ribosomal RNA of rrnB operon
Reads supporting (aligned to +/- strand):  ref base T (2/3);  new base A (32/39);  total (34/42)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTT  >  NC_000913/4168445‑4168636                                                                                                |                                                                                                 ccACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAg                                                                                              <  2:68471/100‑1 (MQ=255) ccACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAg                                                                                              >  1:651444/1‑100 (MQ=255)  cACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGc                                                                                             <  2:179912/100‑1 (MQ=255)  cACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGc                                                                                             <  1:346690/100‑1 (MQ=255)  cACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGc                                                                                             <  1:1363184/100‑1 (MQ=255)      tGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGaa                                                                                         <  2:1409576/100‑1 (MQ=40)      tGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGaa                                                                                         <  2:333819/100‑1 (MQ=255)       gCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGaaa                                                                                        >  1:231138/1‑100 (MQ=255)          ggTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAAtt                                                                                     >  2:301560/1‑100 (MQ=255)              tgtgAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGaaa                                                                                 <  1:1432883/100‑1 (MQ=255)              tgtgAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGaaa                                                                                 <  1:620281/100‑1 (MQ=255)               gtgagtgaAAGTCGCCGACTTTAATATCTCAAATCTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAac                                                                                <  2:392217/100‑1 (MQ=255)               gtgagtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAac                                                                                <  1:1285725/100‑1 (MQ=255)               gtgagtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGAGTGATGTTTGAGATATTTCCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAac                                                                                >  2:1389467/1‑100 (MQ=255)                 gagtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAacac                                                                              >  2:784063/1‑100 (MQ=255)                 gagtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAacac                                                                              >  2:687426/1‑100 (MQ=255)                 gagtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAacac                                                                              >  2:783920/1‑100 (MQ=255)                  ngtaaaaGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGAGATGTTTGAGACATTTGCTCTTTAAAAATCTGGAACAAGCTGAAACTTGAAac                                                                                >  2:331965/5‑97 (MQ=14)                   gtgaAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTg                                                                            >  1:708554/1‑100 (MQ=255)                       aaGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGaaca                                                                        >  2:1475931/1‑100 (MQ=255)                       aaGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTAAAAAATCTGGAACAAGCTGAAAATTGAAACACTGaaca                                                                        <  2:967933/100‑1 (MQ=255)                        aGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGaacaa                                                                       >  2:1424259/1‑100 (MQ=255)                         gTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGaacaac                                                                      <  2:767971/100‑1 (MQ=255)                           cGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACga                                                                    >  1:1325756/1‑100 (MQ=25)                               gACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTCAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAgt                                                                <  2:873138/100‑1 (MQ=255)                                aCCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAgtt                                                               >  2:64263/1‑100 (MQ=18)                                 ccTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAgttg                                                              <  1:1424269/100‑1 (MQ=18)                                 ccTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAACCTGAAAATTGAAACACTGAACAACGAGAgttg                                                              <  1:1493434/100‑1 (MQ=255)                                  cTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAgttgt                                                             >  2:1183261/1‑100 (MQ=18)                                     aaTATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTAGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCg                                                          >  2:1007089/1‑100 (MQ=255)                                      atatCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGt                                                         <  1:649189/100‑1 (MQ=18)                                       tatCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCgcg                                                        >  1:589195/1‑98 (MQ=12)                                         tctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAg                                                      >  2:1256078/1‑100 (MQ=33)                                         tctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAg                                                      >  1:179314/1‑100 (MQ=18)                                         tctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAg                                                      >  1:154099/1‑100 (MQ=17)                                         tctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAg                                                      <  1:64263/100‑1 (MQ=18)                                          ctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGt                                                     >  1:624320/1‑100 (MQ=33)                                          ctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGt                                                     >  1:1112616/1‑100 (MQ=18)                                          ctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGt                                                     >  2:479700/1‑100 (MQ=18)                                          ctcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCCCTTTAAAAATCTGGAACAATCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGt                                                     <  2:856152/100‑1 (MQ=255)                                           tcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGtc                                                    >  2:46436/1‑100 (MQ=18)                                           tcAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGtc                                                    <  2:847851/100‑1 (MQ=17)                                            cAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGtct                                                   >  2:939665/1‑100 (MQ=18)                                              aaaCTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGtctct                                                 <  1:314054/100‑1 (MQ=33)                                                 cTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCaa                                              <  1:9954/100‑1 (MQ=17)                                                       ttCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTc                                        <  2:992020/100‑1 (MQ=17)                                                       ttCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTc                                        <  1:1475941/100‑1 (MQ=18)                                                        tCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCg                                       <  2:624317/100‑1 (MQ=33)                                                        tCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCg                                       <  2:819101/100‑1 (MQ=18)                                                         cGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGc                                      <  2:1501711/100‑1 (MQ=18)                                                         cGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGc                                      <  2:910308/100‑1 (MQ=18)                                                         cGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGc                                      <  1:295254/100‑1 (MQ=17)                                                           ggTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCaa                                    <  2:23732/100‑1 (MQ=18)                                                            gTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAac                                   >  1:325151/1‑100 (MQ=18)                                                                tGTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACga                               <  1:939673/100‑1 (MQ=18)                                                                 gTTTGAGATATTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACgat                              <  2:1229761/100‑1 (MQ=18)                                                                  tttGAGATATTTGCTCTTTAACAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACgatg                             <  2:1207976/100‑1 (MQ=12)                                                                        atatTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAAt                       <  1:1409254/100‑1 (MQ=18)                                                                         tatTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATc                      <  1:1146680/100‑1 (MQ=17)                                                                         tatTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATc                      <  2:712211/100‑1 (MQ=17)                                                                         tatTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATc                      <  1:877857/100‑1 (MQ=18)                                                                         tatTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATc                      <  2:631877/100‑1 (MQ=18)                                                                          atTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCg                     >  2:553679/1‑100 (MQ=18)                                                                          atTTGCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCg                     >  2:140334/1‑100 (MQ=18)                                                                              gCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgaaag                 <  1:784068/100‑1 (MQ=18)                                                                              gCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgaaag                 <  1:783925/100‑1 (MQ=18)                                                                              gCTCTTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgaaag                 <  2:1112609/100‑1 (MQ=18)                                                                                tctTTAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCgaaagaa               <  1:1266525/100‑1 (MQ=18)                                                                                  tttAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAAc             >  2:870604/1‑100 (MQ=17)                                                                                  tttAAAAATCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAAc             >  2:1315398/1‑100 (MQ=17)                                                                                         aTCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCg      >  1:819269/1‑100 (MQ=18)                                                                                          tCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCgg     <  2:702480/100‑1 (MQ=18)                                                                                          tCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCgg     >  1:702483/1‑100 (MQ=18)                                                                                          tCTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCgg     >  1:998705/1‑100 (MQ=18)                                                                                           cTGGAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCggg    >  2:676268/1‑100 (MQ=18)                                                                                             ggAACAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGtt  >  2:778915/1‑100 (MQ=18)                                                                                                |                                                                                                 CCACTTGCTGGTTTGTGAGTGAAAGTCGCCGACCTTAATATCTCAAAACTCATCTTCGGGTGATGTTTGAGATATTTGCTCTTTAAAAATCTGGATCAAGCTGAAAATTGAAACACTGAACAACGAGAGTTGTTCGTGAGTCTCTCAAATTTTCGCAACACGATGATGAATCGAAAGAAACATCTTCGGGTT  >  NC_000913/4168445‑4168636

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: ‑