Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,448,819	C→A	7.4%	P6H (CCC→CAC)	PP_3067 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,448,819	0	C	A	7.4%	155.2 / 2.2	54	P6H (CCC→CAC)	PP_3067	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/25);  new base A (2/2);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.99e-01

AAAAATACGATCATCATCAATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTGACACGAAC  >  NC_002947/3448678‑3448964                                                                                                                                              |                                                                                                                                                   aaaaaTACGATCATCATCAATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTg                                                                                                                                             >  1:123917/1‑149 (MQ=255)  aaaaTACGATCATCATCAATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTg                                                                                                                                             <  7:69981/148‑1 (MQ=255)      tACGATCATCATCAATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCggg                                                                                                                                        >  2:325712/1‑149 (MQ=255)               catcaATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATgg                                                                                                                                 >  4:76668/1‑147 (MQ=255)                atcaATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAg                                                                                                                              <  8:35566/149‑1 (MQ=255)                   aaTGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCa                                                                                                                               <  5:386061/145‑1 (MQ=255)                   aaTGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCa                                                                                                                               >  6:386061/1‑145 (MQ=255)                        cTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCATATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGgc                                                                                                                      <  7:253574/148‑1 (MQ=255)                                cTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGAt                                                                                                              >  3:140451/1‑148 (MQ=255)                                cTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATc                                                                                                             <  4:344235/149‑1 (MQ=255)                                  ttCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCACGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCAt                                                                                                           >  7:187812/1‑149 (MQ=255)                                   tCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCAt                                                                                                           <  5:363047/148‑1 (MQ=255)                                     cGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTa                                                                                                        <  2:123917/149‑1 (MQ=255)                                     cGCTTGGGCGGAAGCAAAGACGGGGCTCCGCTGGTCCTTGCGTGCTAGCCAGGCCTATAACAGCTCTCCCTTGGTCACGCTAGCTTCACATGATTACGCCTATTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTa                                                                                                        <  8:348450/149‑1 (MQ=255)                                      gCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTaa                                                                                                       <  7:91555/149‑1 (MQ=255)                                      gCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTaa                                                                                                       <  7:365978/149‑1 (MQ=255)                                               gAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGgcgc                                                                                                                    >  6:124793/1‑127 (MQ=255)                                               gAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGgcgc                                                                                                                    <  5:124793/127‑1 (MQ=255)                                                 aGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTccc                                                                                            <  1:115659/149‑1 (MQ=255)                                                  gCAATGACGGGTCTTCTCTGGTGCTTGATTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGAGGGCAAATGGCAGGAT‑ATGAGCCTAGATCATGTAAGGAAGCTTACCt                                                                                           >  3:168200/1‑149 (MQ=255)                                                    aaTGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTg                                                                                         <  8:96139/149‑1 (MQ=255)                                                             gCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAGTGGCTGGAT‑AGGCGGCTAGATCATGTAAGGAAGCTTCCCGTGATATCCCtt                                                                                >  8:252138/1‑149 (MQ=255)                                                               ttCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATAACtttt                                                                              >  1:243292/1‑149 (MQ=255)                                                                  tctGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTccc                                                                           >  2:924/1‑149 (MQ=255)                                                                    tgctgcttgcttgctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGTCAAATGGCAGGAT‑AGGCGCCTAGCTCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTcc                                                                            <  6:283279/143‑1 (MQ=255)                                                                      gTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTa                                                                         <  4:200601/147‑1 (MQ=255)                                                                           tgcttgctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTccc                                                                           >  2:87116/1‑140 (MQ=255)                                                                           tgcttgctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGGCGTGGCGGGCAAATGGCAGGATAAGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTccc                                                                           <  1:87116/141‑1 (MQ=255)                                                                             cttgctAGCCAGGCCTATAACAGCTCTCCATTGGTCACTCTAGCTTAACATTATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTATTAACttt                                                                 <  4:168200/148‑1 (MQ=255)                                                                               tgctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTcc                                                               >  5:81991/1‑148 (MQ=255)                                                                                 ctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTc                                                                >  4:202758/1‑145 (MQ=255)                                                                                 ctAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTc                                                                <  3:202758/145‑1 (MQ=255)                                                                                  tAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTccc                                                              >  4:142383/1‑146 (MQ=255)                                                                                      cAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGc                                                        >  8:121093/1‑148 (MQ=255)                                                                                          ccTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGc                                                   >  2:255417/1‑149 (MQ=255)                                                                                               aaCAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCAATTTCCCAAGAGCGATGCCGATc                                              <  7:60078/149‑1 (MQ=255)                                                                                                   gCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGt                                            >  8:175215/1‑147 (MQ=255)                                                                                                   gCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTaa                                          <  4:333655/149‑1 (MQ=255)                                                                                                    ctctCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAg                                         <  7:175215/149‑1 (MQ=255)                                                                                                     tctcCAGTGGTCACGCTAGATTAACATGATTACGCCTCTTCACGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCATTTTCCCTAGTCAATTTCCAAAGAGCGATGCCGATCGTAAgg                                        >  8:218658/1‑149 (MQ=255)                                                                                                         cAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGgcg                                      <  7:121093/147‑1 (MQ=255)                                                                                                         cAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCt                                    >  4:279269/1‑149 (MQ=255)                                                                                                         cAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCt                                    >  4:107039/1‑149 (MQ=255)                                                                                                           gTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCtgt                                  <  3:76668/149‑1 (MQ=255)                                                                                                              gTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTgg                                >  8:75889/1‑148 (MQ=255)                                                                                                              gTCACGCTAGCTTAACATGATTACGCCTCTTCACGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTggg                               <  8:187812/149‑1 (MQ=255)                                                                                                                  cGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGa                           <  6:166724/149‑1 (MQ=255)                                                                                                                           aaCATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCC‑TTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTc                 >  6:194565/1‑149 (MQ=255)                                                                                                                              aTGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGt               >  5:16842/1‑149 (MQ=255)                                                                                                                                  ttACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGttttt           <  3:142383/149‑1 (MQ=255)                                                                                                                                  ttACGCCTCTTCACGTCGTGGCGGGCAAATGGCAGGAT‑ATTCTCCTAGATCATTTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAATATCGATGCCGATCGTAAGTCGCTGTGTGACGAATGTATTTTCGtttt            <  7:218658/148‑1 (MQ=255)                                                                                                                                    aCGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCCAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTGa         >  4:204271/1‑149 (MQ=255)                                                                                                                                      gCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTcaca       >  2:51939/1‑149 (MQ=255)                                                                                                                                      gCCTCTTCCCGTCGTGGCGGGCAAATGGCACGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTGaca       >  8:116207/1‑149 (MQ=255)                                                                                                                                             cccGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTGACACGAAc  <  1:325712/147‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                   AAAAATACGATCATCATCAATGGCTTAGGAGCTTTCCGCTTGGTCGGAAGCAATGACGGGGCTTCTCTGGTGCTTGCTTGCTAGCCAGGCCTATAACAGCTCTCCAGTGGTCACGCTAGCTTAACATGATTACGCCTCTTCCCGTCGTGGCGGGCAAATGGCAGGAT‑AGGCGCCTAGATCATGTAAGGAAGCTTCCCTTGAAATCCCTTTTCCCTAGTCACTTTCCCAAGAGCGATGCCGATCGTAAGGCGCTGTGGGACGAATGTATTTTCGTTTTTGACACGAAC  >  NC_002947/3448678‑3448964

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: ‑