Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,520,454	A→T	11.8%	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	11.8%	128.8 / 8.1	51	intergenic (+45/+27)	cspD/icd	DNA replication inhibitor/NADP(+)‑specific isocitrate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base A (21/24);  new base T (3/3);  total (24/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.01e-01

CCCCAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTT  >  NC_002947/4520307‑4520600                                                                                                                                                    |                                                                                                                                                    ccccAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTaa                                                                                                                                                    <  3:272329/149‑1 (MQ=255)  cccAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGACAGCGACTTGGGCGAGCCGCAAAGCGAAACTGCAAAATACTGACTTCCTGCGCAGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTat                                                                                                                                                    >  6:335785/1‑147 (MQ=255)          cTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGa                                                                                                                                           >  1:18695/1‑149 (MQ=255)          cTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGa                                                                                                                                           <  3:71842/149‑1 (MQ=255)           ttGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGAc                                                                                                                                          >  2:319488/1‑149 (MQ=255)             gCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGTCAGAGTCTGCAAGATCCTTGGGCTAGCCGCAAAGCGAAACTGCAAAAGCATGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGAc                                                                                                                                          <  7:146891/147‑1 (MQ=255)              cACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAACGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCg                                                                                                                                        <  4:233412/148‑1 (MQ=255)              cACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCg                                                                                                                                        <  7:83538/148‑1 (MQ=255)                    gTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCt                                                                                                                                 <  6:140607/149‑1 (MQ=255)                        aaaTCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGtt                                                                                                                              <  1:132329/148‑1 (MQ=255)                         aaTCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGc                                                                                                                            <  7:97960/149‑1 (MQ=255)                          aTCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTTAAAGAAGCgg                                                                                                                                           >  4:12670/1‑132 (MQ=255)                          aTCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTTAAAGAAGCgg                                                                                                                                           <  3:12670/133‑2 (MQ=255)                              aaGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTaa                                                                                                                                                    >  6:48186/1‑120 (MQ=255)                              aaGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTaa                                                                                                                                                    <  5:48186/120‑1 (MQ=255)                                 aTGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCCCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑tg                                                                                                                   >  6:17834/1‑149 (MQ=255)                                            gCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCAt                                                                                                        <  6:145799/149‑1 (MQ=255)                                                          tGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGc                                                                                          >  3:68765/1‑149 (MQ=255)                                                          tGCCAGAGCCTTGGGAGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACAGGTTTTCTGTTTCCTTAAA‑TGTGTATGATCAATTCATCGCCaaatc                                                                                          >  4:236685/1‑147 (MQ=255)                                                           gCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGTCGCTTCTTTTAaagaa                                                                                                                                               <  5:24650/96‑1 (MQ=255)                                                           gCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGTCGCTTCTTTTAaagaa                                                                                                                                               >  6:24650/1‑96 (MQ=255)                                                            ccAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑t                                                                                                                    >  1:307728/1‑121 (MQ=255)                                                            ccAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑t                                                                                                                    <  2:307728/121‑1 (MQ=255)                                                              agagCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGttt                                                                                                              >  5:196383/1‑125 (MQ=255)                                                              agagCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGttt                                                                                                              <  6:196383/125‑1 (MQ=255)                                                                          gAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTc                                                                                                     <  8:271442/122‑1 (MQ=255)                                                                          gAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTc                                                                                                     >  7:271442/1‑122 (MQ=255)                                                                                        aaCTGCAAAAGCCTGACTGGCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAATACAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGATCTGCTTACCAGCTTGGCGCCCTCCa                                                            <  5:335785/149‑1 (MQ=255)                                                                                          cTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCAt                                                           >  4:301873/1‑148 (MQ=255)                                                                                          cTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATc                                                          <  4:68765/149‑1 (MQ=255)                                                                                              aaaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCTCCCTCCATCAAt                                                       <  3:159139/148‑1 (MQ=255)                                                                                              aaaaGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCACCCTCCATCAAt                                                       >  4:159139/1‑148 (MQ=255)                                                                                                            ctgcGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAg                                        >  1:62384/1‑149 (MQ=255)                                                                                                               cgcTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAgg                                       <  3:301873/147‑1 (MQ=255)                                                                                                               cgcTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAgg                                       <  1:343259/147‑1 (MQ=255)                                                                                                                    tgCCGATATACAAAAAAATCGGACTCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTTCA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCGATCAATCGCTCGAAATCGTAGGTCACg                                  <  3:236685/147‑1 (MQ=255)                                                                                                                    tgCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACg                                  <  4:135309/147‑1 (MQ=255)                                                                                                                          tAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGc                          <  2:18695/149‑1 (MQ=255)                                                                                                                              cAAAAAAATCGGCCGCTGCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACAAGCTTGGCGCCCTCAATCAATCTCTCGAAATCGTAGGTCACGGTCTTGGCCGc                       >  7:132738/1‑148 (MQ=255)                                                                                                                                aaaaaaTCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAAt                    <  5:17834/149‑1 (MQ=255)                                                                                                                                   aaaTCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGgc                 <  1:319488/149‑1 (MQ=255)                                                                                                                                   aaaTCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGgc                 <  2:62384/149‑1 (MQ=255)                                                                                                                                      ccGGTCGCTTCTTTTAAAGAAGCGGCCGGTTTTCTGTTGCCTTACAGTGTGTTTGATCATTTCATCGCCAAAGCCTGAGATGCTTACCAGATTGGCGCCATCCATCAATCGGTCGAAATCGTAGTTAACGGAATTgg                           >  1:80333/2‑137 (MQ=255)                                                                                                                                      ccGGTCGCTTCTTTTAAAGAAGCGGCCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTgg                           <  2:80333/135‑1 (MQ=255)                                                                                                                                         gCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCAtt           >  6:10986/1‑149 (MQ=255)                                                                                                                                           cGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCCCTCGAAATCGTAGGACACGGTCTTGGCCGCAATGCCGCCATTgg         >  8:47636/1‑149 (MQ=255)                                                                                                                                             cttcttTAAAAGAAGCGAACGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCATACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGGCATTGGTg       <  6:192244/149‑1 (MQ=255)                                                                                                                                              ttcttTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGc      >  7:326283/1‑149 (MQ=255)                                                                                                                                                 tttAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCt   >  5:166813/1‑149 (MQ=255)                                                                                                                                                 tttAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCt   >  1:142816/1‑149 (MQ=255)                                                                                                                                                 tttAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGGCTTGGCCGCAATGGCGCCATTGGTGCCCt   >  5:321416/1‑149 (MQ=255)                                                                                                                                                 tttAAAAGAAGCGAACGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTAACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCt   >  7:143666/1‑149 (MQ=255)                                                                                                                                                  ttAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCtt  >  4:321439/1‑149 (MQ=255)                                                                                                                                                   tAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATc                                                                                                  >  4:198279/1‑52 (MQ=255)                                                                                                                                                   tAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATc                                                                                                  <  3:198279/52‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    CCCCAAGGGCTTGCACGCCGTTGAAATCAAAGATGCCGCGGCCGCTGCGGCAGAGGCTGCCAGAGCCTTGGGCGAGCCGCAAAGCGAAACTGCAAAAGCCTGACTGCCTGCGCTGTGCCGATAGACAAAAAAATCGGCCGCTTCTTTAAAAGAAGCGACCGGTTTTCTGTTGCCTTACA‑TGTGTTTGATCATTTCATCGCCAAAGCCTGAGCTGCTTACCAGCTTGGCGCCCTCCATCAATCGCTCGAAATCGTAGGTCACGGTCTTGGCCGCAATGGCGCCATTGGTGCCCTT  >  NC_002947/4520307‑4520600

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: ‑