Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,360,959	A→G	7.3%	D8G (GAC→GGC)	phoP →	two‑component system DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,360,959	0	A	G	7.3%	159.4 / 2.5	56	D8G (GAC→GGC)	phoP	two‑component system DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (27/24);  new base G (2/2);  total (29/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

ACCTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTG  >  NC_002947/1360816‑1361098                                                                                                                                                |                                                                                                                                             aCCTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGAACATGAAACTGCTGGTGGTCGAGGACGAAg                                                                                                                                         >  1:173726/1‑149 (MQ=255)   cTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGcc                                                                                                                                       >  2:74081/1‑149 (MQ=255)      tgCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTg                                                                                                                                    >  4:127539/1‑149 (MQ=255)        cAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGc                                                                                                                                   <  3:127539/148‑1 (MQ=255)             ccTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGTCGAAGCCCTGCTTCGcc                                                                                                                             <  7:48020/149‑1 (MQ=255)                   gTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCAcc                                                                                                                       >  4:193087/1‑149 (MQ=255)                    tttCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCg                                                                                                                               >  7:229489/1‑140 (MQ=255)                    tttCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCg                                                                                                                               <  8:229489/140‑1 (MQ=255)                        tGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTa                                                                                                                   >  5:97613/1‑148 (MQ=255)                                cTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCt                                                                                                          <  6:164994/149‑1 (MQ=255)                                    acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGGCGAAGCAGGGCTTCgtcc                                                                                                                            >  3:221640/1‑124 (MQ=38)                                    acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGGCGAAGCAGGGCTTCgtcc                                                                                                                            >  3:225334/1‑124 (MQ=38)                                    acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGGCGAAGCAGGGCTTCgtcc                                                                                                                            <  4:225334/127‑4 (MQ=38)                                    acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGGCGAAGCAGGGCTTCgtcc                                                                                                                            <  4:221640/127‑4 (MQ=38)                                    acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGc                                                                                                      >  2:108573/1‑149 (MQ=255)                                         tttCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAg                                                                                                 >  8:202608/1‑149 (MQ=255)                                             aGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCgg                                                                                              <  7:202608/148‑1 (MQ=255)                                             aGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCgg                                                                                              <  1:156302/148‑1 (MQ=255)                                                   tgtgCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCAtgtg                                                                                       >  7:210055/1‑149 (MQ=255)                                                     tgCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCAATCACCTCTACACCCGCCTGGGCGAAAGTGGCCATGTG‑Gt                                                                                    >  5:53960/1‑149 (MQ=255)                                                             cTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGc                                                                                                                                   <  5:38673/95‑1 (MQ=255)                                                             cTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGc                                                                                                                                   >  6:38673/1‑95 (MQ=255)                                                             cTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCgg                                                                            <  1:108573/149‑1 (MQ=255)                                                                tgGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCg                                                                         >  7:71325/1‑149 (MQ=255)                                                                  ggAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGc                                                                        <  7:199043/148‑1 (MQ=255)                                                                    aGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGa                                                                     <  3:193087/149‑1 (MQ=255)                                                                    aGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTAGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGa                                                                     <  8:199292/149‑1 (MQ=255)                                                                      cGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATg                                                                   <  8:71325/149‑1 (MQ=255)                                                                             gCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGaa                                                              >  5:236836/1‑147 (MQ=255)                                                                             gCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAaga                                                            <  3:169882/149‑1 (MQ=255)                                                                              cccGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGAGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAagag                                                           >  4:73429/1‑149 (MQ=255)                                                                                cgcgAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCTGTCGCTGATGCCg                                                                <  6:193537/142‑1 (MQ=255)                                                                                cgcgAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCg                                                                >  5:193537/1‑142 (MQ=255)                                                                                 gcgAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCGGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGgcg                                                        <  5:94462/149‑1 (MQ=255)                                                                                   gAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCt                                                      >  5:60784/1‑149 (MQ=255)                                                                                   gAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCt                                                      >  4:60111/1‑149 (MQ=255)                                                                                   gAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGAACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCt                                                      <  2:173726/149‑1 (MQ=255)                                                                                         gCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTAcc                                                 <  6:236836/148‑1 (MQ=255)                                                                                         gCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCa                                                <  6:97613/149‑1 (MQ=255)                                                                                                   gCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAg                                      >  7:123855/1‑149 (MQ=255)                                                                                                       tACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTAcc                                  <  3:60111/149‑1 (MQ=255)                                                                                                            aTAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTGATTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCAttt                              <  1:74081/149‑1 (MQ=255)                                                                                                            aTAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTc                             <  4:205476/149‑1 (MQ=255)                                                                                                            aTAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTc                             >  3:205476/1‑149 (MQ=255)                                                                                                              aaGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGa                           >  5:197630/1‑149 (MQ=255)                                                                                                               aGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGTGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGa                           <  6:53960/148‑1 (MQ=255)                                                                                                                    cTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGc                     <  8:210055/149‑1 (MQ=255)                                                                                                                          aTGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCcatcat               >  8:13149/1‑149 (MQ=255)                                                                                                                           tGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAgg                                              <  5:144050/117‑1 (MQ=255)                                                                                                                           tGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAgg                                              >  6:144050/1‑117 (MQ=255)                                                                                                                            gAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCatcatc              >  8:99431/1‑148 (MQ=255)                                                                                                                             aaaCTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGa            >  7:47322/1‑149 (MQ=255)                                                                                                                               aCTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGCCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGAc           >  8:192015/1‑148 (MQ=255)                                                                                                                                 tgctgGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTg        >  6:231228/1‑149 (MQ=255)                                                                                                                                    tggtggTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGc     >  4:206168/1‑149 (MQ=255)                                                                                                                                       tggtCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTg  <  8:47322/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                             ACCTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTG  >  NC_002947/1360816‑1361098

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: ‑