Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,079,596	A→T	10.9%	intergenic (‑67/+5)	PP_t54 ← / ← PP_t53	tRNA‑Arg/tRNA‑Arg

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,079,596	0	A	T	10.9%	122.8 / 2.1	48	intergenic (‑67/+5)	PP_t54/PP_t53	tRNA‑Arg/tRNA‑Arg
Reads supporting (aligned to +/- strand):  ref base A (25/17);  new base T (3/3);  total (28/20)
Fisher's exact test for biased strand distribution p-value = 6.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTTATAAAACAAC  >  NC_002947/5079456‑5079742                                                                                                                                             |                                                                                                                                                     cGGACTCAGCTGGATTCGAACCTGCGACCGTTGGGGTCGTATCCGTGTACTCTATCCAGCTGTGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGc                                                                                                                                             <  1:324417/149‑1 (MQ=255) cGGACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGc                                                                                                                                             <  5:144025/149‑1 (MQ=255)        aggagGTTTCGATACTGCGATCGCTCGTCTCGTATCCTATTAATTTATCCATATGATCTATGAGTCCTCAATTGGCAGTTTAAGACATTATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTc                                                                                                                                      <  6:160146/145‑1 (MQ=255)        agcacGATGCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTca                                                                                                                                     <  7:321300/149‑1 (MQ=255)                 cGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCaaa‑a                                                                                                                                                  <  7:304713/128‑1 (MQ=255)                 cGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCaaa‑a                                                                                                                                                  >  8:304713/1‑128 (MQ=255)                            cctctctGTTAGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCTAAATTGGTACTTTTACACCAGATATCGCTTTTTGATTTAAGCATTTTTTCAAAGAAAGCCTCTTCTAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGAc                                                                                                                 <  2:391721/146‑1 (MQ=17)                                  ggTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCg                                                                                                           <  3:399389/149‑1 (MQ=255)                                   tttCGTAGCCGAGTACTCTATCCAGCTTAGCTATGAGTCGGTTTTTGGCTGTTTAAGACATTATACCGCTGGTTGATTCAAGCAGCCTTTCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCgg                                                                                                          <  6:200485/148‑1 (MQ=18)                                              aGTACTCTATTCAGCTGATATTTTATTGGGCAATTGGCAGTTTTACACCATATCCCTCTGGTTTATTGAAGAAGACTTGCTAACTAACTCTTTTCTAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGa                                                                                               <  8:121190/149‑1 (MQ=12)                                                        ccAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTa                                                                                            <  8:97907/142‑1 (MQ=255)                                                        ccAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTa                                                                                            >  7:97907/1‑142 (MQ=255)                                                        ccAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTa                                                                                            <  4:224020/142‑1 (MQ=255)                                                        ccAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTa                                                                                            >  3:224020/1‑142 (MQ=255)                                                        ccAGCTGAGCTATGAGTCCGAAATTTGCAGGGATTTAAAAGAGACGGCTGGATGATTGAAGCAGCCTTTAAGACATAG‑CACAAGAAATAGTGGAGG‑AGTCAGATGGATTCGAACATCCGAACTAACGGTTGGTAGCGGGGTAGTCTATc                                                                                     >  8:164385/1‑149 (MQ=255)                                                                  tATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGAAGCCATGCAAACAAAGACACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGATCGGTTCGTAGCCGAGTACTATATCCAGATGAGc                                                                            >  5:318870/1‑148 (MQ=18)                                                                    ttaGTCCCGAATTGGCTCTTTTAGACATTATCCCGCTGGGTGATTCATGCAGCCTTGAAAACAAAGCCACTTCTAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTAt                                                                         <  6:183216/147‑1 (MQ=17)                                                                    tGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTAt                                                                         >  7:224316/1‑149 (MQ=255)                                                                     gAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTAt                                                                         >  8:177200/1‑148 (MQ=255)                                                                       gTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAg                                                                      <  7:177200/149‑1 (MQ=255)                                                                        tCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGt                                                                     >  2:377636/1‑149 (MQ=255)                                                                          cGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTcc                                                                   >  5:138664/1‑149 (MQ=255)                                                                            cAATTAGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTg                                                                               <  2:358852/135‑1 (MQ=255)                                                                            cAATTAGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTg                                                                               >  1:358852/1‑135 (MQ=255)                                                                               ttGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCATTGCAAACAAAGCAACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTc                                                              >  5:285644/1‑149 (MQ=255)                                                                                  gCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGGGCTATGAGTCCGTGTCTTg                                                           >  7:143333/1‑149 (MQ=255)                                                                                            aCCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGGCAAAAAGCAGGATTAGAACCTGCGACCCCAAGGTTCGTAGCCGAGTAATAAAACCAGCTGAGGTATGAGTCCGGTTATTGCCGCGCAt                                                   >  1:319390/1‑148 (MQ=255)                                                                                                gATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAgg                                             >  2:241643/1‑149 (MQ=255)                                                                                                     cGCTTGTTGATTGAAGCAGCATTGCTAACAAAGCCTCTTCAAA‑TGTGGCGG‑ACTCAGCATGATTCGAACCTGCGACCTCGCGTTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCt                                        <  6:318870/149‑1 (MQ=21)                                                                                                     cGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCt                                        >  6:3487/1‑149 (MQ=255)                                                                                                      gCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCt                                        >  1:29923/1‑148 (MQ=255)                                                                                                        tGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtata                                               >  6:185103/1‑139 (MQ=255)                                                                                                        tGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtata                                               <  5:185103/139‑1 (MQ=255)                                                                                                          gTTGATTGAAGCAGCCTTGCAATCAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCa                                                    <  5:386702/132‑1 (MQ=255)                                                                                                          gTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGaaa                                    <  5:3487/148‑1 (MQ=255)                                                                                                          gTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTAGTAGCCGAGTAATCTATCCAGCTTAGCTATGAGTCCGTCTCTTGCCGCGCa                                                    >  6:386702/1‑132 (MQ=255)                                                                                                              attgaAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGACACAttt                               >  7:147830/1‑149 (MQ=255)                                                                                                                              aaacaaaGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtata                                               >  6:326497/1‑117 (MQ=255)                                                                                                                              aaacaaaGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtata                                               <  5:326497/117‑1 (MQ=255)                                                                                                                              aaacaaaGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTc               >  2:407083/1‑149 (MQ=255)                                                                                                                                acaaaGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGAATCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCAATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCga             >  8:275253/1‑148 (MQ=255)                                                                                                                                    cgCCACTTTTGA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTtat          >  5:8803/2‑148 (MQ=255)                                                                                                                                    cgCCACTTTTGA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTtat          >  5:262773/2‑148 (MQ=255)                                                                                                                                     gCCACTTTTGA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGAATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTtata         >  4:384893/1‑148 (MQ=255)                                                                                                                                          ttCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtat                                                <  4:300032/104‑1 (MQ=255)                                                                                                                                          ttCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATtat                                                >  3:300032/1‑104 (MQ=255)                                                                                                                                          ttCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTTATAAaacaa   >  5:88278/1‑149 (MQ=255)                                                                                                                                            cAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCtt                  <  2:113008/132‑1 (MQ=255)                                                                                                                                            cAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCtt                  >  1:113008/1‑132 (MQ=255)                                                                                                                                            cAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTTATAAaacaac  >  3:78689/1‑148 (MQ=255)                                                                                                                                             |                                                                                                                                                     CGGACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGCAATTGGCAGTTTTAGACCAGATACCGCTGGTTGATTGAAGCAGCCTTGCAAACAAAGCCACTTCAAA‑AGTGGCGG‑ACTCAGCAGGATTCGAACCTGCGACCGCTCGGTTCGTAGCCGAGTACTCTATCCAGCTGAGCTATGAGTCCGTGTCTTGCCGCGCATTATAGGTCGCTGAAACATTTTTGCAAGAAGCTTTTCGTTATAAAACAAC  >  NC_002947/5079456‑5079742

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑