Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,165	A→C	17.8%	intergenic (‑129/‑139)	PP_5175 ← / → PP_5176	HlyD family secretion protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,903,165	0	A	C	17.8%	96.4 / 15.2	50	intergenic (‑129/‑139)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (16/25);  new base C (4/5);  total (20/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

ACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903022‑5903310                                                                                                                                                 |                                                                                                                                                   aCGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTATTAGCGGGCGCGGCcg                                                                                                                                               >  4:307083/1‑149 (MQ=255)  cGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTTGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTAATAGAGGGCGAGccccc                                                                                                                                              >  7:155720/1‑147 (MQ=255)    cATAAACGCCATGCTGGCTCCTTGCTTGAGCACAAATTATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGTCATTTTTGGTGCCTTCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGa                                                                                                                                            <  7:154988/149‑1 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCcgcg                                                                                                                                             >  1:118511/1‑147 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                              <  6:55077/146‑1 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCcgc                                                                                                                                              >  5:55077/1‑146 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGaa                                                                                                                                           <  2:118511/149‑1 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGaa                                                                                                                                           <  5:383945/149‑1 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGAGGGCGAGCCcgcg                                                                                                                                             >  4:60890/1‑147 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACACCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCcgcg                                                                                                                                             >  4:141632/1‑147 (MQ=255)     aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGAGGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCGCTTCGCGGGCTCGCCCGCGaa                                                                                                                                           <  3:35332/149‑1 (MQ=255)     aTCAACGCAATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCACTTCCCGGGCGAGCCcccg                                                                                                                                             >  7:50976/1‑147 (MQ=255)           gCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGcc                                                                                                                                     >  7:5208/1‑149 (MQ=255)           gCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTATTCGCGGGCGAGCCCGCGAAGAGGc                                                                                                                                      >  8:269654/1‑148 (MQ=255)                        cttgcttgTGAACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCAt                                                                                                                          <  4:360829/147‑1 (MQ=255)                            cttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACACCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCa                                                                                                                    <  3:141632/149‑1 (MQ=255)                            cttgTGAACAATTTTTTTGTGGTTTGCGACGGTGAGGGTTGTTCTGGTTTCGATAAACATCACTTCCGGGGGCCTTGTTGTCTTTTTTGTTGCCTGCGG‑GGGCCTCTTCGGGGGGGAGCCCGCTATGAGGCCTCCACAGCCATGTATc                                                                                                                     <  8:50976/148‑1 (MQ=255)                             ttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGa                                                                                                                                                    >  5:139213/1‑116 (MQ=255)                             ttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGa                                                                                                                                                    <  6:139213/116‑1 (MQ=255)                               gtgCACAAATGTTTTGTGGGATGCTCCTGTGAGCGTAGTTCAGGGTTCTATAAACATCACTGTCGGGGGCCTTGCTGGCATTTTTGGTGCCTGCGGCGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCa                                                                                                                    <  1:102160/147‑1 (MQ=255)                                tgCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCTCGCCCGCGAaga                                                                                                                                         >  6:395278/1‑124 (MQ=255)                                tgCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCTCGCCCGCGAaga                                                                                                                                         <  5:395278/124‑1 (MQ=255)                                    caAATGATTTGTGGGATGCGACTGTGCGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGc                                                                                                            <  8:114094/149‑1 (MQ=255)                                        tGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCata                                                                                                        >  2:255454/1‑149 (MQ=255)                                            ttGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGTAGATGCGTCCACAGCCATGTa                                                                                                                       >  6:103009/1‑130 (MQ=255)                                            ttGGGGGCTGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTCCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTa                                                                                                                       <  5:103009/130‑1 (MQ=255)                                                    tGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCAt                                                                                           <  1:255454/149‑1 (MQ=255)                                                            tgAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCAt                                                                                    <  8:5208/148‑1 (MQ=255)                                                                 gTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCg                                                                                  <  8:90803/145‑1 (MQ=255)                                                                 gTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCg                                                                                  >  7:90803/1‑145 (MQ=255)                                                                        aGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCCCGAACAGGCCTCCACAGCCATGTATAAGTATCTGGCATATCCAGAA‑ACCATCACGCATCGGCCATCCCCGt                                                                       >  1:17317/1‑149 (MQ=255)                                                                          ggTTCGATAAACATCACTGAGGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAAGACCATCAGGCATCGGCCATCCCCGtt                                                                      <  1:212044/149‑1 (MQ=255)                                                                          ggTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCa                                                                                         <  3:38073/129‑1 (MQ=255)                                                                               gATAAACATCCCTGACGGGGGCCATGCTGGCATTTTTGGGGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAAc                                                                 <  3:307083/148‑1 (MQ=255)                                                                               gATAAACATCACTGACGGGGGCCATGCTGTCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAAcc                                                                <  2:298211/149‑1 (MQ=255)                                                                                 tAAACATCCTGGCCGGGGCCCATGGTGGCTTTTTTGGGGCGGGGGG‑GGGCCGTTGGGCGGGCGCGCCGGGTATGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCg                                                               <  4:227401/148‑1 (MQ=255)                                                                                                 gggCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCACATCGCCGGCGAGCCCCCGAAGAGGCCGCCACAGCCCTGTATAAGTATATTCCCAATACACAA‑ACCAAAACGCAAAGGCCATACCCCTTACAACCCCGACCATTGACAAGGAg                                              >  2:6551/1‑149 (MQ=255)                                                                                                  ggCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAgg                                             <  7:20025/149‑1 (MQ=255)                                                                                                             cATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa                                  <  1:71051/149‑1 (MQ=255)                                                                                                             cATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTAGCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa                                  <  7:269654/149‑1 (MQ=255)                                                                                                              cctatctgTGCCTGCGG‑GGGCATCTTCGCGGGCGAGCCCGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCaa                                  <  7:161098/141‑1 (MQ=255)                                                                                                                                gggCCTGTTCGCGGGCTAGCCGGCTAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGt                <  8:155720/149‑1 (MQ=255)                                                                                                                                    ctctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAgg                                <  1:258214/129‑1 (MQ=255)                                                                                                                                    ctctTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAgg                                >  2:258214/1‑129 (MQ=255)                                                                                                                                     tctTCGCGCGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCAAATCCAGAA‑ACCAACAGGCATCGGCCATCCCCGTTCCAACCCCTACCTATCACAGGGAGCCTCACATTCAAGGAAGATCAAAATGCCGATAGcc           >  6:204890/1‑149 (MQ=255)                                                                                                                                      ctTCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGc                                            <  4:383741/115‑1 (MQ=255)                                                                                                                                      ctTCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGc                                            >  3:383741/1‑115 (MQ=255)                                                                                                                                       ttCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAg                             >  6:140716/1‑129 (MQ=255)                                                                                                                                       ttCGCGGGCTCGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAg                             <  5:140716/129‑1 (MQ=255)                                                                                                                                       ttCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg          >  6:258736/1‑148 (MQ=255)                                                                                                                                          gcgGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAACATCAAAATGCCGTTAGCCGAAt       <  3:60890/148‑1 (MQ=255)                                                                                                                                              gCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAc  <  1:6551/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                   ACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGG‑GGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCACAGCCATGTATCAGTATCTGCCATATCCAGAA‑ACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903022‑5903310

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: ‑