Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,931,867	C→T	7.4%	intergenic (‑140/+31)	apeB ← / ← rluA	M18 family aminopeptidase/bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,931,867	0	C	T	7.4%	156.3 / 2.4	55	intergenic (‑140/+31)	apeB/rluA	M18 family aminopeptidase/bifunctional tRNA pseudouridine(32) synthase TrmQ/ribosomal large subunit pseudouridine synthase RluA
Reads supporting (aligned to +/- strand):  ref base C (25/25);  new base T (2/2);  total (28/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.99e-01

ACTCCAGACAGCAGTGGCGCGAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGCGGGTTG  >  NC_002947/1931733‑1932012                                                                                                                                       |                                                                                                                                                  aCTCCAGACAGCAGTGGCGCGAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGcc                                                                                                                                       <  5:197058/147‑1 (MQ=255)           gcagTGGCGCGAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCt                                                                                                                           <  8:25582/149‑1 (MQ=255)              gTGGCGCGAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGc                                                                                                                         >  8:166238/1‑148 (MQ=255)                   gcgAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAAt                                                                                                                    >  7:148149/1‑148 (MQ=255)                       gTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGaa                                                                                                               <  7:25884/149‑1 (MQ=255)                              gCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTGCAGGCCCTGCAAAATCAGAACGgcg                                                                                                          >  1:44783/1‑147 (MQ=255)                               cAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAg                                                                                                       >  6:69050/1‑149 (MQ=255)                                 gAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGGACAGGCCCTGCAAAATCAGAACGGCGCAggg                                                                                                     <  7:166238/149‑1 (MQ=255)                                    tGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCAc                                                                                                  >  5:311308/1‑149 (MQ=255)                                        gACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCg                                                                                               <  6:311308/148‑1 (MQ=255)                                         aCAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGc                                                                                                                         <  6:355482/121‑1 (MQ=255)                                         aCAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGaa                                                                                             >  7:14162/1‑149 (MQ=255)                                             tttGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGaa                                                                                                                                             >  1:309289/1‑97 (MQ=255)                                             tttGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGaa                                                                                                                                             <  2:309289/97‑1 (MQ=255)                                                     tGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTg                                                                                 >  1:207748/1‑149 (MQ=255)                                                       cATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGaa                                                                                                               <  3:198233/117‑1 (MQ=255)                                                       cATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGaa                                                                                                               >  4:198233/1‑117 (MQ=255)                                                         tCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCg                                                                             >  1:52509/1‑149 (MQ=255)                                                           ttCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGa                                                                           >  1:64711/1‑149 (MQ=255)                                                             cGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCg                                                                             <  8:14162/145‑1 (MQ=255)                                                                     aCCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCgggt                                                                   <  2:64711/147‑1 (MQ=255)                                                                       ccccGCTACCACAGGTATTGCACCGCCCCTGCGCGCAGTGCGGCCCGTGCAGGAGCGGCGGTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAGTCAGAACGGCGCAGGGCAGTCGAACTTCAACCGCTGCCCGGACCCCgggggggt                                                               >  4:1399/1‑149 (MQ=255)                                                                               ccACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCa                                                       <  5:69050/149‑1 (MQ=255)                                                                                  caGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGc                                                     >  8:124720/1‑148 (MQ=255)                                                                                  caGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCa                                                    >  6:251926/1‑149 (MQ=255)                                                                                      tATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGa                                                <  5:251926/149‑1 (MQ=255)                                                                                      tATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGa                                                <  7:124720/149‑1 (MQ=255)                                                                                        ttGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGTCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGTCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAg                                               <  3:1399/148‑1 (MQ=255)                                                                                        ttGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAgg                                              <  8:148149/149‑1 (MQ=255)                                                                                           cacaGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCgggtggg                                                                <  2:23783/128‑1 (MQ=255)                                                                                           cacaGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCAt                                           >  1:312319/1‑149 (MQ=255)                                                                                            acaGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATg                                          >  4:161004/1‑149 (MQ=255)                                                                                                ccccTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAgg                                      >  5:220553/1‑149 (MQ=255)                                                                                                 cccTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAg                                               >  7:130448/1‑139 (MQ=255)                                                                                                 cccTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAg                                               <  8:130448/139‑1 (MQ=255)                                                                                                  ccTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGa                                                                           <  6:73854/110‑1 (MQ=255)                                                                                                  ccTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGca                                    >  4:133750/1‑149 (MQ=255)                                                                                                      aGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGc                                <  3:161004/149‑1 (MQ=255)                                                                                                            gTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCa                          >  8:225688/1‑149 (MQ=255)                                                                                                                 gCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATgg                       >  5:353861/1‑147 (MQ=255)                                                                                                                 gCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATgg                       <  6:353861/147‑1 (MQ=255)                                                                                                                   ccTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGgccg                   >  6:136433/1‑149 (MQ=255)                                                                                                                   ccTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGgccg                   >  6:216194/1‑149 (MQ=255)                                                                                                                       gCAGGAGCGGCTTTAGTCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAg               >  6:137343/1‑149 (MQ=255)                                                                                                                       gCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAg               >  7:184084/1‑149 (MQ=255)                                                                                                                         aGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAggg             >  6:27933/1‑149 (MQ=255)                                                                                                                         aGGAGCGGCTTAAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCCGAACGGCGCAGGTCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAggg             <  3:217910/149‑1 (MQ=255)                                                                                                                              cGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGc        <  2:207748/149‑1 (MQ=255)                                                                                                                                gCTTTAGTCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGgcc                    >  3:19007/1‑135 (MQ=255)                                                                                                                                gCTTTAGTCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGgcc                    <  4:19007/135‑1 (MQ=255)                                                                                                                                gCTTTAGTCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGCgg      <  5:137343/149‑1 (MQ=255)                                                                                                                                gCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAg                                       <  3:202912/116‑1 (MQ=255)                                                                                                                                gCTTTAGACGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAg                                       >  4:202912/1‑116 (MQ=255)                                                                                                                                    tAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGCGGGtt   <  7:225688/148‑1 (MQ=255)                                                                                                                                     aGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGCGGGTTg  <  6:220553/148‑1 (MQ=255)                                                                                                                                       |                                                                                                                                                  ACTCCAGACAGCAGTGGCGCGAGTTTAACGCAGAATGTCGACAATTTGTGTCTGCATCTTCGCAGCTAACCCCCGCTACCACAGGTATTGCACAGCCCCTGAGCGCAGTGCGGCCCTTGCAGGAGCGGCTTTAGCCGCGAAGAGGCCGGTACAGGCCCTGCAAAATCAGAACGGCGCAGGGCACTCGAACTTCAACCGCTGCCCGGACACCGGGTGGGTAAAGCTCAGCATCGAGGCATGCAGGCACAGCCGCTCATGGGCCGCCAGGGCTTGCGGGTTG  >  NC_002947/1931733‑1932012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑