Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,790,143	A→T	9.0%	intergenic (+22/+46)	ynfM → / ← PP_5073	efflux transporter/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,790,143	0	A	T	9.0%	147.6 / 3.9	53	intergenic (+22/+46)	ynfM/PP_5073	efflux transporter/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (22/26);  new base T (2/3);  total (24/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.51e-01

CGGCGGGCGGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTG  >  NC_002947/5789997‑5790289                                                                                                                                                     |                                                                                                                                                     cggcggGCGGGGTGTTCTGGCACCAGTGCGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCAcc                                                                                                                                                    <  8:160650/149‑1 (MQ=255)  ggcgggcgGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCAccc                                                                                                                                                   <  6:293489/149‑1 (MQ=255)  ggcgggcgGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCAGCAcc                                                                                                                                                    >  6:254766/1‑148 (MQ=255)  ggcgggccGGGTGTTCTGGCACAAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCAACCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCAcc                                                                                                                                                    >  2:100149/1‑148 (MQ=255)               ttCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGa                                                                                                                                      <  2:168518/149‑1 (MQ=255)                     cACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACACCCGCTCCCACAGGTTGTGGGT‑‑GCgggc                                                                                                                              <  6:23364/149‑2 (MQ=39)                          gTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAGCCTGTGGGA‑‑GCGGGTGTGAc                                                                                                                         >  6:29573/1‑149 (MQ=255)                          gTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGAc                                                                                                                         <  7:288229/149‑1 (MQ=255)                                   gAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCATGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAagag                                                                                                                <  8:232593/149‑1 (MQ=255)                                   gAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAagag                                                                                                                <  3:189759/149‑1 (MQ=255)                                     aCGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTGCCTCATTGCACCACATCCAGCTGCCACCCAAAACGGTGTGATGCATTCCTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAaga                                                                                                                 <  1:112387/148‑1 (MQ=255)                                        ggATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCAGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCat                                                                                                           <  5:254766/149‑1 (MQ=255)                                           tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑g                                                                                                                                   <  7:20060/122‑1 (MQ=255)                                           tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCat                                                                                                           >  4:318270/1‑146 (MQ=255)                                           tCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTCTGGGA‑‑g                                                                                                                                   >  8:20060/1‑122 (MQ=255)                                             gggCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGGG‑‑GCGTGGCACCTGAGCAAGTTGCCACCCAAAACGGGGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                      <  1:175562/149‑1 (MQ=255)                                                 tGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                      >  7:82889/1‑145 (MQ=255)                                                 tGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCatcagat                                                                                                      <  8:82889/145‑1 (MQ=255)                                                      aTTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAGCCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTtgatg                                                                                             <  5:29573/149‑1 (MQ=255)                                                        tGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTgatgat                                                                                           >  7:43620/1‑149 (MQ=255)                                                            aGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGCGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                            <  5:250612/112‑1 (MQ=255)                                                            aGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGCGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                            >  6:250612/1‑112 (MQ=255)                                                                     gCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatcc                                                                              <  3:344682/149‑1 (MQ=255)                                                                           gCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                         >  5:1905/1‑148 (MQ=255)                                                                            cgttGATGGTG‑‑GCGTTGCAGCTGAGCAAGTTGCCACCCAAAACGGTTTGATGCATTCGTGGGCACGCGCGCACCCACAACCTGTGGGACCTCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacacc                                                                         <  1:100149/147‑3 (MQ=255)                                                                                    gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                            <  1:170206/88‑1 (MQ=255)                                                                                    gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGgtgt                                                                                                                            >  2:170206/1‑88 (MQ=255)                                                                                    gtg‑‑gCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCg                                                                <  6:1905/148‑1 (MQ=255)                                                                                                    gAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCtt                                                 >  8:133379/1‑149 (MQ=255)                                                                                                     aGCAAGTTGCCACCCAAAACGTTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatc                                                                               <  3:269461/118‑1 (MQ=255)                                                                                                     aGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatc                                                                               >  4:269461/1‑118 (MQ=255)                                                                                                          gTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGtc                                                    >  2:292926/1‑139 (MQ=255)                                                                                                           ttGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAAcc                                          <  2:286231/149‑1 (MQ=255)                                                                                                                 cccAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAAAATCCACATCCACTTCCCGGCTCATCATGTGCTTTTAAACCTAAcc                                     >  8:46462/1‑148 (MQ=255)                                                                                                                   cAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGt                                  >  6:341973/1‑149 (MQ=255)                                                                                                                    aaaaCGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                 <  7:133379/149‑1 (MQ=255)                                                                                                                        cGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCt                             <  8:43620/149‑1 (MQ=255)                                                                                                                           tgtgATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                         >  1:24530/1‑102 (MQ=255)                                                                                                                           tgtgATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATatccacatc                                                                         <  2:24530/102‑1 (MQ=255)                                                                                                                                 gCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTACTTTTCAACCTCACCGGTCAGCTTCACCTTgg                    >  4:202676/1‑149 (MQ=255)                                                                                                                                  cATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTgg                    >  4:255997/1‑148 (MQ=255)                                                                                                                                     tCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCtt                >  5:325792/1‑149 (MQ=255)                                                                                                                                      cGTGGTCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCtt                <  7:46462/148‑1 (MQ=255)                                                                                                                                      cGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTg               >  5:130094/1‑149 (MQ=255)                                                                                                                                       gTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGt              <  6:325792/149‑1 (MQ=255)                                                                                                                                         ggtcacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCg            >  8:160097/4‑149 (MQ=38)                                                                                                                                          ggCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGt           >  3:72539/1‑149 (MQ=255)                                                                                                                                          ggCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGt           <  6:130094/149‑1 (MQ=255)                                                                                                                                            cacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGCGTGCCCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                 >  6:60566/1‑125 (MQ=37)                                                                                                                                            cacaCCCGCTCCCACAGGTTGTGGGT‑‑GCGGGCGTGCCCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTc                                 <  5:60566/125‑1 (MQ=37)                                                                                                                                             acacccGCTCCCACAGGTTGTGGGT‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGa        <  7:160097/146‑1 (MQ=39)                                                                                                                                                 ccGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGGCTTGTCGTTTCACgg    >  6:164805/1‑149 (MQ=255)                                                                                                                                                   gCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTCCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGgtg  <  3:202676/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CGGCGGGCGGGGTGTTCTGGCACCAGTGGGGCTGGAACGGGATCGGGCTGTTCATTGGCAGCTTGCTGGCGGTGGCCTTGATGGTG‑‑GCGTTGCACCTGAGCAAGTTGCCACCCAAAACGGTGTGATGCATTCGTGGGCACGCCCGCACCCACAACCTGTGGGA‑‑GCGGGTGTGACCACGAAGAGGCCATCAGATCAGTTGATGATCTCGACAATATCCACATCCACTTCCCGGCTCATCAGGTGCTTTTCAACCTCACCGGTCAGCTTCACCTTGGTCTTGTCGTTGAACGGTG  >  NC_002947/5789997‑5790289

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: ‑