Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,812,775	C→T	13.5%	intergenic (+69/‑41)	rplT → / → pheS	50S ribosomal protein L20/phenylalanine‑‑tRNA ligase subunit alpha

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,812,775	0	C	T	13.5%	126.6 / 10.6	52	intergenic (+69/‑41)	rplT/pheS	50S ribosomal protein L20/phenylalanine‑‑tRNA ligase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (25/19);  new base T (4/3);  total (29/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.45e-01

GGTTCTGGCTGATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGCAAGAAGGG  >  NC_002947/2812628‑2812922                                                                                                                                                    |                                                                                                                                                     ggTTCTGGCTGATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCt                                                                                                                                                     <  6:123016/149‑1 (MQ=255) ggTTCTGGCTGATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCt                                                                                                                                                     >  4:220221/1‑149 (MQ=255)      tGGCTGATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCa                                                                                                                                                  >  6:313321/1‑147 (MQ=255)           gATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCTTTGAAGGctct                                                                                                                                           >  8:112502/1‑149 (MQ=255)               tGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCCCCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTacc                                                                                                                                       >  6:327775/1‑149 (MQ=255)                 gCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCTTTGAAGGCTCTTcc                                                                                                                                        <  7:112502/146‑1 (MQ=255)                 gCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCTTTGAAGGCTCTTc                                                                                                                                         <  6:261931/145‑1 (MQ=255)                    gTGAACGAAAAAGCGGCGTTTTCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCTCGACAATCACACGGAGGTGCTAGCGCTGCCGGGCATTGAAAGTCATAGATAGCGGAAGAGCCTTCAAAGCTCTTCCCCTAtt                                                                                                                                  >  4:179002/1‑149 (MQ=255)                    gTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTAtt                                                                                                                                  <  3:71209/149‑1 (MQ=255)                       aaCGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTc                                                                                                                               <  1:239102/149‑1 (MQ=255)                       aaCGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTc                                                                                                                               <  6:122766/149‑1 (MQ=255)                         cGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCCTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCaaa                                                                                                                                                >  3:230497/1‑130 (MQ=255)                         cGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCCTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCaaa                                                                                                                                                <  4:230497/130‑1 (MQ=255)                                                      agaAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGa                                                                                               >  7:231631/1‑149 (MQ=255)                                                       gaAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGAt                                                                                              <  3:220221/149‑1 (MQ=255)                                                          aGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCTTTGAAGGCTCTTc                                                                                                                                         >  3:132963/1‑104 (MQ=255)                                                          aGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCTTTGAAGGCTCTTc                                                                                                                                         <  4:132963/104‑1 (MQ=255)                                                           gCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATgcgc                                                                                          <  5:330189/149‑1 (MQ=255)                                                             tAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTg                                                                                        >  5:161333/1‑149 (MQ=255)                                                              aaaGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTgg                                                                                       >  5:219649/1‑149 (MQ=255)                                                               aaGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTg                                                                                        <  3:29990/147‑1 (MQ=255)                                                                          gCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGccc                                                                           <  5:313321/149‑1 (MQ=255)                                                                          gCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGc                                                                             <  4:231840/147‑1 (MQ=255)                                                                                gTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAgg                                                                     >  3:46222/1‑149 (MQ=255)                                                                                     cgcgACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTg                                                                <  3:37314/149‑1 (MQ=255)                                                                                           aaTCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAACACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAAcgc                                                          >  7:106355/1‑149 (MQ=255)                                                                                           aaTCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGtctc                                                                                   >  2:253262/1‑124 (MQ=255)                                                                                            aTCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAAcgcg                                                         <  6:161333/149‑1 (MQ=255)                                                                                               aCCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCACAAGCCCTAGAGGCCGTGGAACGCGCt                                                       >  4:45963/1‑148 (MQ=255)                                                                                                cccGGCAGCGCTAGCACCGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGt                                                                 >  8:297221/1‑137 (MQ=255)                                                                                                cccGGCAGCGCTAGCACCGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGt                                                                 <  7:297221/137‑1 (MQ=255)                                                                                                 ccGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGaa                                                    <  8:231631/149‑1 (MQ=255)                                                                                                    gcggTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGAc                                                 <  6:236482/149‑1 (MQ=255)                                                                                                      ggTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACAt                                               <  4:46222/149‑1 (MQ=255)                                                                                                            aGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGACCTAGAGGCCGTGGAACGCCCTGAAGACATCAACGc                                         >  3:260584/1‑149 (MQ=255)                                                                                                                cTGCCGGGCATTGATCGTCATCGATAGGGGAAGAGCCTTCTAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTg                                     <  5:327775/149‑1 (MQ=255)                                                                                                                     gggCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGaa                                  >  2:142736/1‑147 (MQ=255)                                                                                                                     gggCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCATAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGaa                                  >  8:146188/1‑147 (MQ=255)                                                                                                                     gggCATTGAACGACATCGATAGGGGAAGAGCCTTCAAAGCTCTTACGCTATATTCGTATATGGAGTCTGT‑ACATGGAAAACCTGGCTGCGCTGGTATCCCAAGACCTAGAGCCCGTGGAACGCGCTGAAGACATCAACGCCATGGaa                                  >  8:118695/1‑147 (MQ=255)                                                                                                                            gagcGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGTTGCGCTGGTCTCCCAAGCGCTAGGGGCCGTGGCACGCGCTGAAGCCCTCAACGCCCTGGAAGAGATCggg                         >  6:243326/4‑149 (MQ=255)                                                                                                                              aCGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCggg                        <  3:45963/148‑1 (MQ=255)                                                                                                                                    tCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAAtt                  <  6:322494/148‑1 (MQ=255)                                                                                                                                    tCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAAtt                  >  5:322494/1‑148 (MQ=255)                                                                                                                                    tCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTa                 >  7:66591/1‑149 (MQ=255)                                                                                                                                           gggAAGAGCTTTGAAGGCTCTTCCCCTATTTTCGTATCTGGAGTCTGTGACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGATGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCg            >  1:76395/1‑148 (MQ=255)                                                                                                                                           gggAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCgg           >  8:66228/1‑148 (MQ=255)                                                                                                                                            ggAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGc          >  2:140977/1‑148 (MQ=255)                                                                                                                                            ggAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGc          >  1:47030/1‑148 (MQ=255)                                                                                                                                              aaGAGCTTTGAAGGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGc          >  6:200597/1‑146 (MQ=255)                                                                                                                                              aaGAGCATTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCAGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCATGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCTGGTTAATTATCTCGGCaag       <  7:118695/149‑1 (MQ=255)                                                                                                                                               agagCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGAaag       >  8:142538/1‑148 (MQ=255)                                                                                                                                                gagCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGCaag       >  8:126239/1‑147 (MQ=255)                                                                                                                                                   ccTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGCAAGAAggg  >  4:129623/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GGTTCTGGCTGATCTGGCAGTGAACGAAAAAGCGGCGTTTGCTGCGATTGTCGAGAAAGCTAAAGCCGTTCTGGCTTAAGTACCCGCGACAATCACCCGGCGGTGCTAGCGCTGCCGGGCATTGAACGTCATCGATAGGGGAAGAGCCTTCAAAGCTCTTCCCCTATTTTCGTATCTGGAGTCTGT‑ACATGGAAAACCTGGATGCGCTGGTCTCCCAAGCCCTAGAGGCCGTGGAACGCGCTGAAGACATCAACGCCCTGGAACAGATCCGGGTTAATTATCTCGGCAAGAAGGG  >  NC_002947/2812628‑2812922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑