Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,100,833	G→C	7.7%	W236S (TGG→TCG)	PP_3608 →	LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,100,833	0	G	C	7.7%	157.5 / 3.9	52	W236S (TGG→TCG)	PP_3608	LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base C (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.71e-01

CCTGCCAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTG  >  NC_002947/4100688‑4100977                                                                                                                                                  |                                                                                                                                                  cctgccAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTgg                                                                                                                                                  <  6:94507/147‑1 (MQ=255) cctgccAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGa                                                                                                                                                 <  8:13209/148‑1 (MQ=255) cctgccAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGa                                                                                                                                                 <  6:258721/148‑1 (MQ=255) cctgccAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAg                                                                                                                                                <  7:184517/149‑1 (MQ=255)       aGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCgg                                                                                                                                           >  3:122695/1‑148 (MQ=255)               tatGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTg                                                                                                                                                   >  3:182414/1‑132 (MQ=255)               tatGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTg                                                                                                                                                   <  4:182414/132‑1 (MQ=255)                   gCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCGCACTCCAGTGTGGCaa                                                                                                                                        <  1:271537/139‑2 (MQ=255)                   gCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCGCACTCCAGTGTGGCaa                                                                                                                                        >  2:271537/1‑138 (MQ=255)                            gACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCAc                                                                                                                     >  2:178748/1‑149 (MQ=255)                                                  tATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGcc                                                                                              <  4:122695/149‑1 (MQ=255)                                                            cATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCa                                                                                                                      >  6:74933/1‑116 (MQ=255)                                                            cATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCa                                                                                                                      <  5:74933/116‑1 (MQ=255)                                                                cgcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTggg                                                                                <  7:83182/149‑1 (MQ=255)                                                                 gcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAc                                                                                                                 >  6:221251/1‑116 (MQ=255)                                                                 gcCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAc                                                                                                                 <  5:221251/116‑1 (MQ=255)                                                                   ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                            <  4:8814/103‑1 (MQ=255)                                                                   ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                            <  4:3957/103‑1 (MQ=255)                                                                   ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                            >  3:8814/1‑103 (MQ=255)                                                                   ccGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTgg                                                                                                                            >  3:3957/1‑103 (MQ=255)                                                                    cGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCg                                                                            <  3:278549/149‑1 (MQ=255)                                                                      gATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGtt                                                                          >  1:277776/1‑149 (MQ=255)                                                                      gATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGtt                                                                          <  1:178748/149‑1 (MQ=255)                                                                           tttCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGACCAGCCGCGCTGTGGGGTCGTTgcgc                                                                      >  1:227584/1‑148 (MQ=255)                                                                                aTGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAaca                                                                 >  8:69627/1‑148 (MQ=255)                                                                                aTGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAaca                                                                 >  5:309033/1‑148 (MQ=255)                                                                                 tGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGAcc                                                                                                                <  6:117375/101‑1 (MQ=255)                                                                                  gAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAac                                                                  >  4:17952/1‑145 (MQ=255)                                                                                  gAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAac                                                                  <  3:17952/145‑1 (MQ=255)                                                                                   aaaTCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACaa                                                              <  7:69627/148‑1 (MQ=255)                                                                                        gAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACt                                                        >  8:25251/1‑149 (MQ=255)                                                                                         cgttgtcACTGGCCGCCCGGGGGTTGCAGCGCCGTATTGGCCTGGGCTTGGCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAGTTGGCGAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGacac                                                         <  1:243925/142‑1 (MQ=255)                                                                                          gCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTgc                                                      <  2:277776/149‑1 (MQ=255)                                                                                            gTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTgcgc                                                    >  3:298723/1‑149 (MQ=255)                                                                                               cACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGACCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAg                                                 <  2:227584/149‑1 (MQ=255)                                                                                                aCTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGt                                                >  3:215885/1‑149 (MQ=255)                                                                                                aCTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGAGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGAGCCAACACAAGACACtacatcgg                                                 >  2:243925/1‑141 (MQ=255)                                                                                                aCTGGCCGACCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGt                                                >  6:204/1‑149 (MQ=255)                                                                                                  tGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCt                                                                                                         >  8:71948/1‑91 (MQ=255)                                                                                                  tGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCt                                                                                                         <  7:71948/91‑1 (MQ=255)                                                                                                                  gCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCa                              >  3:134654/1‑149 (MQ=255)                                                                                                                           tATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGt                     >  4:187500/1‑149 (MQ=255)                                                                                                                             ttGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TCGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGGCACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTc                   >  5:304593/1‑149 (MQ=255)                                                                                                                             ctGCCCGGCCCTTGCCCCTCTGGCGTGGGGCAGTCGAAGTGCTGGCCGGCACCGAGCTGATCCTGACAG‑TGGCCAGCCGCGCTGGGGGTTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTc                   <  4:36918/148‑1 (MQ=255)                                                                                                                                cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACt                                   <  6:19980/130‑1 (MQ=255)                                                                                                                                cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACt                                   >  5:19980/1‑130 (MQ=255)                                                                                                                                cccTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGa                 <  6:309033/148‑1 (MQ=255)                                                                                                                                  cTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTa              >  4:327287/1‑149 (MQ=255)                                                                                                                                     gCCTTGCCACTCTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATc            <  6:304593/148‑1 (MQ=255)                                                                                                                                     gCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATc            <  4:215885/148‑1 (MQ=255)                                                                                                                                        ttGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGCCCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGc         >  5:67760/1‑148 (MQ=255)                                                                                                                                          gCCGCACTCCAGTGTGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTgg                                 >  7:296903/1‑122 (MQ=255)                                                                                                                                          gCCGCACTCCAGTGTGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTgg                                 <  8:296903/122‑1 (MQ=255)                                                                                                                                          gCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCaa       <  5:204/148‑1 (MQ=255)                                                                                                                                              cacTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTg  <  7:25251/149‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                  CCTGCCAGTGGCGATATGGCCCTGGAAGACTGGCTGGCACGCCCACATGTATTGATGGCCATGCGCCCGGATGCTTTCGATGAAATCGAGCGTGCACTGGCCGCCCGGGGCTTGCAGCGCCGTATTGCCCTGGCCTTGCCACACTGGAGTGCGGCAGTCGAAGTGCTGGCCGGCACCGACCTGATCCTGACAG‑TGGCCAGCCGCGCTGTGGGGTCGTTGCGCCAACACAAGACACTGCGCCAGTTCACACCGCCACTGGCCATCCCCTCGTTCGACTATCAGCAAGCCTG  >  NC_002947/4100688‑4100977

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: ‑