Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,360,966	C→A	7.1%	A10A (GCC→GCA)	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	1,360,966	0	C	A	7.1%	175.3 / 3.3	56	A10A (GCC→GCA)	phoP	two‑component system DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (26/26);  new base A (2/2);  total (28/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

CTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTGCCCGGTATCAG  >  NC_002947/1360818‑1361109                                                                                                                                                     |                                                                                                                                                 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                                                                                                                                          <  8:229489/140‑1 (MQ=255)                  tttCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCg                                                                                                                                          >  7:229489/1‑140 (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                                                                                                                                       <  4:221640/127‑4 (MQ=38)                                  acaGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGGCGAAGCAGGGCTTCgtcc                                                                                                                                       <  4:225334/127‑4 (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                                                                                                                                              >  6:38673/1‑95 (MQ=255)                                                           cTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGc                                                                                                                                              <  5:38673/95‑1 (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)                                                                                                                                               cGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTGCCCGGTATCa   <  7:99431/149‑1 (MQ=255)                                                                                                                                                gAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTGCCCGGTATCAg  >  3:89405/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                 CTGTGCAGTGCCTTGGGTTTCTGCAGGTGCTACACAGGTTTCAGGGACTGTGCGATTACTGTGGGAGCGGGCGTGCCCGCGAAAGGGCCGGTACAGGCAATACACATAAGGAGCTGCACATGAAACTGCTGGTGGTCGAGGACGAAGCCCTGCTTCGCCATCACCTCTACACCCGCCTGGGCGAAAGCGGCCATGTG‑GTCGAGGCGGTCGCTGATGCCGAAGAGGCGCTGTACCAGGCCGAGCAGTACCATTTCGACCTTGCCATCATCGACCTGGGCCTGCCCGGTATCAG  >  NC_002947/1360818‑1361109

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: ‑