Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,050,223	G→A	7.8%	G362D (GGT→GAT)	spoT →	bifunctional (p)ppGpp synthase/hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,050,223	0	G	A	7.8%	145.1 / 2.3	51	G362D (GGT→GAT)	spoT	bifunctional (p)ppGpp synthase/hydrolase
Reads supporting (aligned to +/- strand):  ref base G (23/24);  new base A (2/2);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.97e-01

ATGCACGGCGTGCCCATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGCCGTC  >  NC_002947/6050075‑6050362                                                                                                                                                      |                                                                                                                                               aTGCACGGCGTGCCCATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAg‑gg                                                                                                                                                >  7:279609/1‑149 (MQ=255)           tGCCCATCGAAATCCAGCTTCGCCCCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GATACCCTT‑‑Gac                                                                                                                                    <  2:155992/149‑2 (MQ=255)              ccATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATTGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTg                                                                                                                                >  6:289623/1‑149 (MQ=255)              ccATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTg                                                                                                                                <  1:122898/149‑1 (MQ=255)               cATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTg                                                                                                                                >  6:143831/1‑148 (MQ=255)                aTCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGAGGGCCAACAACGGCATCGCCGCGCACTGGCTGGACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTgca                                                                                                                              <  5:309372/149‑1 (MQ=255)                      aTCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTTTCCTT‑‑GA‑ACTGCAGCAACg                                                                                                                        >  3:63959/1‑149 (MQ=255)                       tCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGt                                                                                                                       <  5:143831/149‑1 (MQ=255)                         cAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACCACCGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCACCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTg                                                                                                                      <  8:140142/148‑1 (MQ=255)                             ttCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCgg                                                                                                                  >  2:76190/1‑148 (MQ=255)                                gCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAAc                                                                                                              >  4:279119/1‑149 (MQ=255)                                              gAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCAt                                                                                                <  2:65950/149‑1 (MQ=255)                                                  agaTTGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCgag                                                                                            <  5:289623/149‑1 (MQ=255)                                                  agaTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATc                                                                                               >  1:229053/1‑146 (MQ=255)                                                   gaTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGaa                                                                                                     >  6:69827/1‑139 (MQ=255)                                                   gaTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGaa                                                                                                     <  5:69827/139‑1 (MQ=255)                                                    aTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCCCGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGagag                                                                                          >  1:42225/1‑149 (MQ=255)                                                    aTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATc                                                                                               >  3:196476/1‑144 (MQ=255)                                                    aTGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATc                                                                                               <  4:196476/144‑1 (MQ=255)                                                     tGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAGCTGGATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCgaga                                                                                           <  1:76190/148‑1 (MQ=255)                                                       gacaacaaCGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCg                                                                                        <  3:277809/146‑1 (MQ=255)                                                       gCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCg                                                                                        <  1:86162/148‑1 (MQ=255)                                                        ccAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGt                                                                                       >  8:4456/1‑148 (MQ=255)                                                         caacaaCGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTg                                                                                      >  8:236615/1‑148 (MQ=255)                                                         caacaaCGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTg                                                                                      >  8:103972/1‑148 (MQ=255)                                                          aacaacGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCaa                                                                                                               <  3:47438/122‑1 (MQ=255)                                                          aacaacGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCaa                                                                                                               >  4:47438/1‑122 (MQ=255)                                                          aacaacGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTg                                                                                      >  7:240924/1‑147 (MQ=255)                                                           acaacGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTg                                                                                      >  2:20817/1‑146 (MQ=255)                                                               cGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCg                                                                               <  7:4456/149‑1 (MQ=255)                                                                  cATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGATGGG‑GGGGGACTTGGGAGGATACAGCAACGTCCCGGCAACTCACTGGAATTAATCGAGAGAGTGAATATc                                                                                >  1:253405/1‑148 (MQ=255)                                                                   aTCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCt                                                                           <  3:71781/149‑1 (MQ=255)                                                                                         aGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACgtg                                                     <  8:279609/149‑1 (MQ=255)                                                                                           tCAATCGAGGAGGAGGAGCGCTAGGGCAGCCACGGGCGCTCGCGCCAGTGGGTCATG‑GGTATGCTT‑‑GA‑ACTTCAGCAACGTGGCGGCATCTCGCTGTAATTCATCGAGAGCGTGATGATCGACCTGTTCCCGGACGAGGTCTACgtgt                                                    <  8:240924/148‑1 (MQ=255)                                                                                           tCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGtt                                                   <  7:236615/149‑1 (MQ=255)                                                                                             aaaCGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCa                                                 >  2:279031/1‑149 (MQ=255)                                                                                                 gacgacgaGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGcc                                             >  4:122357/1‑149 (MQ=255)                                                                                                 gacgacgaGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGcc                                             >  4:19408/1‑149 (MQ=255)                                                                                                                aaGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCACCTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGATCACGCCCAAAGGCCGGATCAt                              >  3:17894/1‑149 (MQ=255)                                                                                                                 aGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATg                             <  7:103972/149‑1 (MQ=255)                                                                                                                 aGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATg                             <  1:20817/149‑1 (MQ=255)                                                                                                                   ggCAGTCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGa                           >  7:96429/1‑149 (MQ=255)                                                                                                                   ggCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATg                             >  4:35196/1‑147 (MQ=255)                                                                                                                               cgcgcCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAgg               <  2:229053/149‑1 (MQ=255)                                                                                                                               cgcgcCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAgg               <  3:122357/149‑1 (MQ=255)                                                                                                                                        ctgcagttCAAG‑GATACCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGc      >  2:15622/8‑149 (MQ=255)                                                                                                                                           tGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGCCgg   <  2:253405/149‑2 (MQ=255)                                                                                                                                           tGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGCCGt   <  8:96429/149‑1 (MQ=255)                                                                                                                                           cagttCAAG‑GATACCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGcc     <  1:15622/143‑1 (MQ=255)                                                                                                                                             gttCAAG‑GATACCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGCCGTc  >  7:218987/3‑148 (MQ=255)                                                                                                                                                 aaG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATg                             <  2:82760/117‑1 (MQ=255)                                                                                                                                                 aaG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATg                             >  1:82760/1‑117 (MQ=255)                                                                                                                                                      |                                                                                                                                               ATGCACGGCGTGCCCATCGAAATCCAGATTCGCACCCGCGAAATGGAAGAGATGGCCAACAACGGCATCGCCGCGCACTGGCTGTACAAGTCAAACGACGACGAGCAGCCCAAGGGCAGCCACGCGCGCGCCCGCCAGTGGGTCAAG‑GGTATCCTT‑‑GA‑ACTGCAGCAACGTGCCGGCAACTCCCTGGAATTCATCGAGAGCGTGAAGATCGACCTGTTCCCGGACGAGGTCTACGTGTTCACGCCCAAAGGCCGGATCATGGAGTTGCCCAAAGGCTCCACGGCCGTC  >  NC_002947/6050075‑6050362

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑