Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,903,164	G→T	13.5%	intergenic (‑128/‑140)	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	5,903,164	0	G	T	13.5%	122.6 / 8.1	56	intergenic (‑128/‑140)	PP_5175/PP_5176	HlyD family secretion protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/27);  new base T (4/4);  total (24/32)
Fisher's exact test for biased strand distribution p-value = 7.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.70e-01

AGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903017‑5903310                                                                                                                                                    |                                                                                                                                                    aGCTGACGCAGCAACGCCATGCTGGCTCATTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGa                                                                                                                                                    <  7:347037/149‑1 (MQ=255)   cGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGc                                                                                                                                                  <  6:365766/149‑1 (MQ=255)   cGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGc                                                                                                                                                  <  6:98981/149‑1 (MQ=255)     gACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGccc                                                                                                                                                <  1:188065/149‑1 (MQ=255)         cATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGTTGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGa                                                                                                                                            <  6:268471/149‑1 (MQ=255)          aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCGCTTAGCCGGGGCGCCcccg                                                                                                                                             >  3:187122/1‑147 (MQ=255)          aTCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACAGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGaa                                                                                                                                           <  2:233086/149‑1 (MQ=255)           tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTATTCGCGGGCGCGCCcgcg                                                                                                                                             >  8:168952/1‑146 (MQ=255)           tCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGAGGCCTCTTCGCGGGCTCGCCCGCGAag                                                                                                                                          <  7:142356/149‑1 (MQ=255)             aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTTTGGTATGCGACTGTGTGCGTAGTTCTGGGTTCGATTAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCTCGCCCGCGAaga                                                                                                                                         <  1:197449/148‑1 (MQ=255)             aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAagag                                                                                                                                        <  3:168549/149‑1 (MQ=255)             aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAaga                                                                                                                                         <  3:361319/148‑1 (MQ=255)             aaCGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAaga                                                                                                                                         <  2:77205/148‑1 (MQ=255)               cGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGc                                                                                                                                      <  4:156668/149‑1 (MQ=255)                 ccATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTTAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCt                                                                                                                                    <  1:67971/149‑1 (MQ=255)                     gCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCATAGCGGGCGCGCCCGCGAAGAGGCCTCca                                                                                                                                 >  3:125856/1‑148 (MQ=255)                         gCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTTACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGcc                                                                                                                           <  8:98435/149‑1 (MQ=255)                           tCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCAt                                                                                                                         >  4:118483/1‑149 (MQ=255)                                gcttgTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTAt                                                                                                                     >  4:339618/1‑148 (MQ=255)                                      gCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCa                                                                                                                          <  6:379708/137‑1 (MQ=255)                                      gCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCa                                                                                                                          >  5:379708/1‑137 (MQ=255)                                         caAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGc                                                                                                           <  1:86878/149‑1 (MQ=255)                                          aaaTGATTTGTGGGATGCGACTGTAAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGGGGCCGCGAAGAGGCCGCCA‑CCGCCAAGTATAAGTATATGc                                                                                                           >  7:16721/1‑148 (MQ=255)                                           aaTGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCa                                                                                                         >  7:23576/1‑149 (MQ=255)                                                          gCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCGGGAATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCAt                                                                                           <  4:152800/148‑1 (MQ=255)                                                           ctaatgtgtgGGTTGTTCCGGGTTGGTTAAACATCACTGACGGGGGCCATGCTTGCATTTTTTGTGCCTGGGGGGGCCTCTTGGCGGGCTAGCCCGCGAAGAGGCCTCCATCAGCCATGTATCAGTATCTGCCATATCCAGAAACCAt                                                                                           <  1:66989/144‑1 (MQ=255)                                                            gACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGGGCGCCCGCGCAGAGGCCGCCC‑CAGCCAAGTATGAGTATATGCCCAATACAGAAACCaac                                                                                          >  2:140641/1‑145 (MQ=255)                                                                         gTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATc                                                                            <  1:140641/148‑1 (MQ=255)                                                                          ttCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATccc                                                                          >  6:333136/1‑149 (MQ=255)                                                                            cAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGCGCGAGCCCCCGAAGAGGCCTCCA‑CCGGCAAGTATAAGTATCTGCCATATCCCGAAACCATCCGGCATCGGCCATACCCg                                                                        >  7:258562/1‑149 (MQ=255)                                                                               ggTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCAATTAGCGGGCGAGCCCGCGAAGAGGCCGCCA‑CAGCCAAGTTTCAGTATATGGCATATACAGAAACCAAAAGGCCTAGGCCATACCCggta                                                                     >  2:105826/1‑146 (MQ=255)                                                                                     aTAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCg                                                               <  1:250931/149‑1 (MQ=255)                                                                                      tAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGc                                                              <  3:339618/149‑1 (MQ=255)                                                                                        aaCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGCGCCCGCGCAGCGGCCTGCC‑CAGCCAAGGTTAAGTATCTGCCATATACAGAAACCCACACGCCTCGGCCCTCCCCCTTGCCAcccgga                                                            >  4:279608/1‑145 (MQ=255)                                                                                         aCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGGCCGCGAAGAGGCCTCCA‑CAGCCAAGTATCAATATCTGCCAAATACAGAAACCATAAGGCATCGGCCAAACCCCTTCCAACCCCTAc                                                           >  2:249591/1‑149 (MQ=255)                                                                                         aCATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTAc                                                           <  1:105826/149‑1 (MQ=255)                                                                                          cATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGTGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCgg                                                                                 <  1:235317/126‑1 (MQ=255)                                                                                              ccTGCCGGGGCCCTTGCGGGCTTTTTTGGGGCCTGGGGGGGCCTCTTCGCGGGCGAGCCCGCTAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTc                                                      <  4:187122/148‑1 (MQ=255)                                                                                               cTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTca                                                     <  3:118483/149‑1 (MQ=255)                                                                                                  aCGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGGATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAg                                                  <  1:249591/149‑1 (MQ=255)                                                                                                    gggggCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAggg                                                <  8:23576/149‑1 (MQ=255)                                                                                                                 gCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTc                                                      <  7:264350/130‑1 (MQ=255)                                                                                                                 gCATTTTTGGTGCCTGCGGGGGCCTCTTAGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCAAGTATCAGTATATGCCATATCCAGAAACCATCAGGCAACGGCCATCCCCGTTACAACCCCTACCATTc                                                      >  8:264350/1‑130 (MQ=255)                                                                                                                     ttttGGTGCCTGCGGGGGCCTCTTCGCGTGCTCCCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAgg                                <  3:240805/148‑1 (MQ=255)                                                                                                                                     ggCCTCTTCGCGGGCGAGCCCGCTAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGtt               <  7:168952/149‑1 (MQ=255)                                                                                                                                      gCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGt                >  2:191657/1‑147 (MQ=255)                                                                                                                                      gCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCAAGTATCAGTATATGCCATATACAGAAACCATCAGGCATCGGCCCTACCCGTTACAACCGCTACCGTTCACAAGGAGGCAAACAATAAAGGAAGAACAAAATGCCGt                >  4:70488/1‑147 (MQ=255)                                                                                                                                        ctctTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCTGTTAGc            >  5:52136/1‑149 (MQ=255)                                                                                                                                        ctctTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGc            >  5:266421/1‑149 (MQ=255)                                                                                                                                         tctTCGCGGGCTCGCCCGCGAAGCGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc           >  1:276602/1‑149 (MQ=255)                                                                                                                                         tctTCGCGGGCTCGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc           >  8:304145/1‑149 (MQ=255)                                                                                                                                         tctTCGCGGGCTCGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGcc           >  3:6519/1‑149 (MQ=255)                                                                                                                                           ttCGCGGGCTCGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg          >  2:74493/1‑148 (MQ=255)                                                                                                                                           ttCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCg          >  1:355221/1‑148 (MQ=255)                                                                                                                                              gcgGGCCAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAAt       <  5:231334/148‑1 (MQ=255)                                                                                                                                                  gCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAc  <  4:125856/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                    AGCGGACGCATCAACGCCATGCTGGCTCCTTGCTTGTGCACAAATGATTTGTGGGATGCGACTGTGAGCGTAGTTCAGGGTTCGATAAACATCACTGACGGGGGCCATGCTGGCATTTTTGGTGCCTGCGGGGGCCTCTTCGCGGGCGAGCCCGCGAAGAGGCCTCCA‑CAGCCATGTATCAGTATCTGCCATATCCAGAAACCATCAGGCATCGGCCATCCCCGTTCCAACCGCTACCTTTCACAGGGAGGCTCACATTCAAGGAAGATCAAAATGCCGTTAGCCGAATGCCAC  >  NC_002947/5903017‑5903310

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: ‑