Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,406,095	C→A	12.9%	Y71* (TAC→TAA)	PP_2110 →	ribosomal large subunit pseudouridine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,406,095	0	C	A	12.9%	78.4 / 4.5	31	Y71* (TAC→TAA)	PP_2110	ribosomal large subunit pseudouridine synthase
Reads supporting (aligned to +/- strand):  ref base C (14/13);  new base A (2/2);  total (16/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.26e-01

GTGCCTGCCTCCTGGTAACTGGGTGACGGTGCTCGATTGCTTGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTCCTGCCGGTGACGCCGACCGGTGAATACGTC  >  NC_002947/2405948‑2406242                                                                                                                                                    |                                                                                                                                                    gtgCCTGCCTCCTGGTAACTGGGTGACGGTGCTCGATTGCTTGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACaa                                                                                                                                                   >  1:166918/1‑150 (MQ=255) gtgCCTGCCTCCTGGTAACTGGGTGACGGTGCTCGATTGCTTGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTGGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACaa                                                                                                                                                   >  1:430910/1‑150 (MQ=255)    cctgcctCCTGGTAACTGGGTGACGGTGCTCGATTGCTTGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCg                                                                                                                                                >  1:201308/1‑150 (MQ=255)                                         ttGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTg                                                                                                                                              <  1:256962/115‑1 (MQ=255)                                         ttGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTg                                                                                                                                              >  2:256962/1‑115 (MQ=255)                                         ttGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCcgaac                                                                                                           >  2:289085/1‑150 (MQ=255)                                         ttGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCcgaac                                                                                                           <  2:201308/150‑1 (MQ=255)                                            tgtgACCATGTCAAGGCCATCGACCGCGCCCAGTGGCTTGCACACATGTACCGTGGCCGGGTGCTGGATGCAAAGGGTCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCcgaacgaa                                                                                                        <  1:594326/150‑1 (MQ=255)                                                 ccATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGcc                                                                                                   <  2:409074/150‑1 (MQ=255)                                                                 gACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCaggag                                                                                   >  1:283055/1‑150 (MQ=255)                                                                    gtcgcgCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAggtg                                                                                >  2:550450/3‑150 (MQ=255)                                                                       gcCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGgtggtg                                                                             <  2:166918/150‑1 (MQ=255)                                                                                  tGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCcgaacgaa                                                                                                        <  2:254421/112‑1 (MQ=255)                                                                                  tGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCcgaacgaa                                                                                                        >  1:254421/1‑112 (MQ=255)                                                                                     ccGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGa                                                               <  1:566185/150‑1 (MQ=255)                                                                                      cGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTAAAAGCGTGGCATGCGTTTGCATTACTTcc                                                                                                                         <  1:130939/91‑1 (MQ=255)                                                                                      cGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTAAAAGCGTGGCATGCGTTTGCATTACTTcc                                                                                                                         <  1:434907/91‑1 (MQ=255)                                                                                      cGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTAAAAGCGTGGCATGCGTTTGCATTACTTcc                                                                                                                         >  2:130939/1‑91 (MQ=255)                                                                                      cGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTAAAAGCGTGGCATGCGTTTGCATTACTTcc                                                                                                                         >  2:434907/1‑91 (MQ=255)                                                                                               cGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCtggtg                                                     <  2:283055/150‑1 (MQ=255)                                                                                                gTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCtggtgg                                                    <  2:430910/150‑1 (MQ=255)                                                                                                     cGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGcc                                               >  2:158737/1‑150 (MQ=255)                                                                                                        gTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGAt                                            >  1:321348/1‑150 (MQ=255)                                                                                                                   cAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTCGACGAGCACCTGGTGGTGGCCGATAAACCGCAttt                                 >  2:202413/1‑150 (MQ=255)                                                                                                                      ggggCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTCCt                              <  2:321348/150‑1 (MQ=255)                                                                                                                       gggCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTcc                               >  1:482039/1‑148 (MQ=255)                                                                                                                       gggCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTcc                               <  2:482039/148‑1 (MQ=255)                                                                                                                         gcaggcagTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCg                                                                                            <  1:29620/85‑1 (MQ=255)                                                                                                                         gcaggcagTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCg                                                                                            >  2:29620/1‑85 (MQ=255)                                                                                                                                             tGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACAGCATTTCCTGCCGGTGACGCCGACCGGTGAAt       >  1:35791/1‑150 (MQ=255)                                                                                                                                                  tACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTCCTGCCGGTGACGCCGACCGGTGAATACGTc  <  1:550450/150‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    GTGCCTGCCTCCTGGTAACTGGGTGACGGTGCTCGATTGCTTGTGTGACCATTTCAAGGCCATCGACCGCGCCCAGTGGCTTGACCGCTTTGCCCGTGGCCGGGTGCTGGATGCCAAGGGGCAGGCAGTTGCCGCCGACCTGCCTTACAAGCGTGGCATGCGTTTGCATTACTTCCGCGAAGTGCCGAACGAACGGCCGATTCCGGTGCAGGAGGTGGTGCTGCATGTGGACGAGCACCTGGTGGTGGCCGATAAACCGCATTTCCTGCCGGTGACGCCGACCGGTGAATACGTC  >  NC_002947/2405948‑2406242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑