Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,520,454	A→T	12.5%	intergenic (+45/+27)	cspD → / ← icd	DNA replication inhibitor/NADP(+)‑specific isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,520,454	0	A	T	12.5%	106.0 / 8.0	48	intergenic (+45/+27)	cspD/icd	DNA replication inhibitor/NADP(+)‑specific isocitrate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base A (22/20);  new base T (4/2);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 6.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.87e-01

CCCCAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTTGA  >  NC_002947/4520307‑4520602                                                                                                                                                     |                                                                                                                                                     ccccAAGGGCTTGCACGACGTTGAAATCAAAGATGCCGCGGCCGCTGCGTCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTTACTGCCTGCTCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTGTTTaa                                                                                                                                                     <  5:105494/149‑1 (MQ=255)   ccAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTaa                                                                                                                                                     >  7:15231/1‑147 (MQ=255)   ccAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTaa                                                                                                                                                     >  3:70877/1‑147 (MQ=255)      aGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAaagaa                                                                                                                                                <  8:15231/149‑1 (MQ=255)       gggCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAaagaag                                                                                                                                               <  5:201644/149‑1 (MQ=255)          cTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTTAAAGAAGCgg                                                                                                                                            <  3:233126/149‑2 (MQ=255)          cTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTTAAAGAAGCGa                                                                                                                                            >  3:179470/1‑149 (MQ=255)              cACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCgg                                                                                                                                        >  2:67182/1‑149 (MQ=255)                cGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGtt                                                                                                                                      <  3:230312/149‑1 (MQ=255)                     ttGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GTCGCTTCTTTTAAAGAAGCGGCCGAttttttt                                                                                                                                 <  4:50528/149‑4 (MQ=39)                        aaaTCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGtt                                                                                                                               <  5:8074/148‑1 (MQ=255)                           tCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCt                                                                                                                           >  3:68614/1‑149 (MQ=255)                             aaaGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGtt                                                                                                                               <  5:1960/143‑1 (MQ=255)                             aaaGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGtt                                                                                                                               >  6:1960/1‑143 (MQ=255)                                     cgcgGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGtt                                                                                                                 <  2:228676/149‑1 (MQ=255)                                         gCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGAt                                                                                                             <  1:127079/149‑1 (MQ=255)                                                    agagGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGc                                                                                                  <  6:247134/149‑1 (MQ=255)                                                             cAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCt                                                                                          >  3:39879/1‑148 (MQ=255)                                                             cAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTg                                                                                         <  8:189326/149‑1 (MQ=255)                                                                         cGAGACGCAAAGCGAATCTGCAAAAGCCTGAGTGCGTGCGCTGTGCCGATAGACAATATAATCG‑GCCGCTTCTTTAAAAGAAGCGAGCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCGAAAGCCTGAGCTGCTTACCa                                                                             <  4:70877/149‑1 (MQ=255)                                                                          gAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGTTCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTAc                                                                               >  1:215569/1‑147 (MQ=255)                                                                               gCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGCGCTGCTTACCAGCTTgg                                                                       >  6:195570/1‑149 (MQ=255)                                                                                cAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTACTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACAAGCTTGgc                                                                      >  7:114470/1‑149 (MQ=255)                                                                                  aaGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGgcgc                                                                    >  1:151796/1‑149 (MQ=255)                                                                                      gAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAg                                                                                       >  4:218491/1‑126 (MQ=255)                                                                                      gAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAg                                                                                       <  3:218491/126‑1 (MQ=255)                                                                                       aaaCTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTg                                                                        <  1:88670/140‑1 (MQ=255)                                                                                       aaaCTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTg                                                                        >  2:88670/1‑140 (MQ=255)                                                                                              aaaaGGCTTACTGCCTGGGCTGTGCCTATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATc                                                        <  5:156704/149‑1 (MQ=255)                                                                                              aaaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATc                                                        >  4:52874/1‑149 (MQ=255)                                                                                              aaaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATc                                                        >  4:120144/1‑149 (MQ=255)                                                                                              aaaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTATCTGTTGCCTTACATGTGATTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGAGCCCTCCATCAATc                                                        >  5:244023/1‑149 (MQ=255)                                                                                               aaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCg                                                       >  4:226557/1‑149 (MQ=255)                                                                                                 aGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCTGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCt                                                     <  4:39879/149‑1 (MQ=255)                                                                                                   ccTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTc                                                    >  8:148067/1‑148 (MQ=255)                                                                                                          gcctgcGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCAt                                                                                                     >  5:244779/1‑92 (MQ=255)                                                                                                          gcctgcGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCAt                                                                                                     <  6:244779/92‑1 (MQ=255)                                                                                                           cctgcGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTa                                           <  3:120144/149‑1 (MQ=255)                                                                                                            ctgcGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAg                                          <  3:226557/149‑1 (MQ=255)                                                                                                                gcTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCTCTCCATCAATCGCTCGAAATCGTAGGTCa                                      >  4:221993/1‑149 (MQ=255)                                                                                                                               aaaaaaaTCG‑GCCGCTTCTTTAAAAGACGCGACCGGGTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCaa                       >  8:145853/1‑149 (MQ=255)                                                                                                                               aaaaaaaTCG‑GCCGCTTCTTTAAAAGAAGCGCCCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCaa                       >  8:72792/1‑149 (MQ=255)                                                                                                                                 aaaaaTCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCa                                                           <  7:160089/111‑1 (MQ=255)                                                                                                                                 aaaaaTCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCa                                                           >  8:160089/1‑111 (MQ=255)                                                                                                                                       cG‑GTCGCTTCTTTTAAAGAAGCGGCCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCa               >  3:77874/1‑149 (MQ=255)                                                                                                                                       cG‑GTCGCTTCTTTTAAAGAAGCGGCCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCa               >  6:36556/1‑149 (MQ=255)                                                                                                                                          gtcGCTTCTTTTAAAGAAGCGGCCGATTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCAtt             >  3:103213/3‑149 (MQ=255)                                                                                                                                           ccGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTc                                       <  3:93828/122‑1 (MQ=255)                                                                                                                                           ccGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTc                                       >  4:93828/1‑122 (MQ=255)                                                                                                                                               ttcttTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGc        >  4:138045/1‑149 (MQ=255)                                                                                                                                                    tAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCTCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCtt    <  3:221993/148‑1 (MQ=255)                                                                                                                                                     aaaaGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTtga  <  5:178122/149‑1 (MQ=255)                                                                                                                                                     aaaaGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTtg   <  8:208286/148‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CCCCAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCG‑GCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACATGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTTGA  >  NC_002947/4520307‑4520602

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: ‑