Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	6,126,947	T→A	9.1%	intergenic (+38/+29)	PP_5374 → / ← PP_5375	choline/carnitine/betaine transporter family protein/LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	6,126,947	0	T	A	9.1%	143.9 / 3.7	52	intergenic (+38/+29)	PP_5374/PP_5375	choline/carnitine/betaine transporter family protein/LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (21/26);  new base A (2/3);  total (23/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CTTCCTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCTGGAGTAC  >  NC_002947/6126808‑6127092                                                                                                                                              |                                                                                                                                                  cTTCCTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCg                                                                                                                                          <  2:63760/149‑1 (MQ=255)    ccTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGt                                                                                                                                        <  3:5117/148‑1 (MQ=255)     cTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCTGATGGCTGTCGGTc                                                                                                                                       <  8:167356/148‑1 (MQ=255)     cTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAAACACAAGACCGACAGCTGATGGCTGTCGGTc                                                                                                                                       <  3:273477/148‑1 (MQ=255)        taCCTGTGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTCGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTtgt                                                                                                                                   <  2:221140/149‑1 (MQ=255)         aCCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAACGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGCCAGCCATCAGCTGTCGGTCTtgtg                                                                                                                                  >  2:126597/1‑149 (MQ=255)            tGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGttt                                                                                                                               >  8:242538/1‑149 (MQ=255)              ggcttCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGtttt                                                                                                                              <  4:52891/145‑1 (MQ=255)                aTTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCCTTTGTCCTTGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTg                                                                                                                             <  1:120021/149‑1 (MQ=255)                 ttCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGc                                                                                                                          <  1:20884/149‑1 (MQ=255)                  tCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAAACACAAGACCGACAGCTGATGGCTGTCGGTCTtgt                                                                                                                                   >  7:2621/1‑139 (MQ=38)                  tCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAAACACAAGACCGACAGCTGATGGCTGTCGGTCTtgt                                                                                                                                   <  8:2621/139‑1 (MQ=38)                      ccGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGc                                                                                                                      >  8:194775/1‑148 (MQ=255)                      ccGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCt                                                                                                                     >  4:251834/1‑149 (MQ=255)                          aaGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTAttt                                                                                                                 <  3:251834/149‑1 (MQ=255)                               aTCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGtttt                                                                                                                              >  8:15579/1‑131 (MQ=255)                               aTCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGtttt                                                                                                                              <  7:15579/131‑1 (MQ=255)                                    gCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGaa                                                                                                       <  7:194775/149‑1 (MQ=255)                                           gCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCATCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAggg                                                                                                <  3:203757/149‑1 (MQ=255)                                                  cc‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCGCCGAAGGCAGGGCCATCaa                                                                                         >  7:244850/1‑149 (MQ=255)                                                         cc‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTc                                                                                   >  1:198885/1‑149 (MQ=255)                                                              cGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCg                                                                                >  2:52974/1‑148 (MQ=255)                                                                         atatGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCAc                                                                    <  1:344387/149‑1 (MQ=255)                                                                              gggCTGACAGCGAAGATAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACACACAGCCAACAGCTTTCGTTCTTGTGTATTGGGCAGGCAATTTCTGCACAGCAGTCAGGGACATCAACCACTACCGAGACAGCCCCaacctt                                                                >  8:90784/1‑143 (MQ=255)                                                                               ggCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCa                                                                                                            >  4:149412/1‑103 (MQ=255)                                                                               ggCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCa                                                                                                            <  3:149412/103‑1 (MQ=255)                                                                                               aGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATc                                                                                           <  1:156832/104‑1 (MQ=255)                                                                                               aGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAgg                                                        >  2:901/1‑139 (MQ=255)                                                                                               aGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAgg                                                        <  1:901/139‑1 (MQ=255)                                                                                                      tAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgac                                        >  2:133747/1‑148 (MQ=255)                                                                                                       aaCCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTTGGCAGGCTATTTCTGCACCGAAGGCACGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgacga                                      >  6:215944/1‑149 (MQ=255)                                                                                                       aaCCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgacga                                      >  6:333313/1‑149 (MQ=255)                                                                                                        aCCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCATCCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgacga                                      <  7:242538/148‑1 (MQ=255)                                                                                                          cTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTc                                   >  8:167968/1‑149 (MQ=255)                                                                                                             aaGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCcag                                <  7:167968/149‑1 (MQ=255)                                                                                                                ccACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgac                                        <  4:60023/138‑1 (MQ=255)                                                                                                                ccACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGgac                                        >  3:60023/1‑138 (MQ=255)                                                                                                                ccACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGga                                         <  6:36619/137‑1 (MQ=255)                                                                                                                ccACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGga                                         >  5:36619/1‑137 (MQ=255)                                                                                                                  aCCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCGCCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAgcaggc                           <  8:244850/149‑1 (MQ=255)                                                                                                                      tGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGaa                       >  8:67703/1‑149 (MQ=255)                                                                                                                             cacaAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGc                 <  2:198885/148‑1 (MQ=255)                                                                                                                             cacaAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCg                <  1:52974/149‑1 (MQ=255)                                                                                                                                aaGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCg             <  4:246682/149‑1 (MQ=255)                                                                                                                                aaGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCg             >  3:246682/1‑149 (MQ=255)                                                                                                                                aaGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCg             <  1:133747/149‑1 (MQ=255)                                                                                                                                  gACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTcc                                                                                  <  7:24184/78‑1 (MQ=255)                                                                                                                                  gACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTcc                                                                                  >  8:24184/1‑78 (MQ=255)                                                                                                                                       aCAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCTGGa      <  7:90784/149‑1 (MQ=255)                                                                                                                                           ccATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCt         >  7:205336/1‑142 (MQ=255)                                                                                                                                           ccATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCt         <  8:205336/142‑1 (MQ=255)                                                                                                                                           ccATCAGCTGTCGGTCTTGTGTTTT‑GGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCTGGAGTAc  >  5:21942/1‑148 (MQ=255)                                                                                                                                              |                                                                                                                                                  CTTCCTATACCTGGGATTCACCCGCAAGGCATCACGCCGGTGGCTGGGCCC‑TTGGCC‑TGCGAGGGGCTTGATATGGGGCTGACAGCGAAGAAAGCCAGCTAACCTAAAGCCACCCTGGAAGACACAAGACCGACAGCCATCAGCTGTCGGTCTTGTGTTTTGGGCAGGCTATTTCTGCACCGAAGGCAGGGCCATCAACCAGTCCCGGAACAGCCGCACGCTTTCACGAGGACCACGCTCGGTGGACGACTCCAGCAGGCAGAACTTGGCGTCGGTCTGGAGTAC  >  NC_002947/6126808‑6127092

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: ‑