Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,866,696	G→T	7.0%	intergenic (+19/+38)	PP_5140 → / ← thyA	MerR family transcriptional regulator/thymidylate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,866,696	0	G	T	7.0%	172.2 / 2.5	57	intergenic (+19/+38)	PP_5140/thyA	MerR family transcriptional regulator/thymidylate synthase
Reads supporting (aligned to +/- strand):  ref base G (27/26);  new base T (2/2);  total (29/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01

AGCTGCGGCGGCGCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGCCAGTTT  >  NC_002947/5866553‑5866840                                                                                                                                                 |                                                                                                                                                 aGCTGCGGCGGCGCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGCTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAAccc                                                                                                                                             <  1:292989/149‑1 (MQ=255)  gCTGCGGCGGCGCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCcg                                                                                                                                            <  4:173202/149‑1 (MQ=255)  gCTGCGGCGGCGCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCcg                                                                                                                                            >  3:173202/1‑149 (MQ=255)        gcggcgCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGaa                                                                                                                                        >  8:281625/1‑147 (MQ=255)           gcacTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGt                                                                                                                                   <  3:115451/146‑1 (MQ=255)             gcTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTTCACCCGCGAagcttttg                                                                                                                                 <  5:21770/149‑7 (MQ=255)              cTGCAACGCGCAGGGGAGCGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTTCACCCGCGAagcttttgg                                                                                                                                <  4:264120/149‑8 (MQ=255)               tGCAAAGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGt                                                                                                                               >  4:218703/1‑149 (MQ=255)                       gcAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACaa                                                                                                                       >  1:153366/1‑149 (MQ=255)                              aGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGAt                                                                                                                <  3:218703/149‑1 (MQ=255)                                       gcgATCTTGCAGCAACTGGAGACAAACGGGGCCGTATCGGTACCGGATACCGAACATTCCCATCT‑GGGGCGGAGTCACGGGCATTCAGCCAAAAGCTTCGCGGGTGAAACCGCGAAGAGGTCAGTTCTAAAAATAGCGATCTATCAGAc                                                                                                       >  3:316992/1‑149 (MQ=255)                                         gATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGAGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCg                                                                                                     >  4:15571/1‑149 (MQ=255)                                             ttGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCTCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCAt                                                                                                 >  7:129178/1‑149 (MQ=255)                                               gcagcaACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGATCCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATc                                                                                                <  1:83389/148‑1 (MQ=255)                                               gcagcaACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCg                                                                                               >  1:198167/1‑149 (MQ=255)                                               gcagcaACTGGAGACAAACGGGGCGGCATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCg                                                                                               >  8:210853/1‑149 (MQ=255)                                                cagcaACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCg                                                                                               <  7:281625/148‑1 (MQ=255)                                                 agcaACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATag                                                                                                                    >  3:54120/1‑126 (MQ=255)                                                 agcaACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATag                                                                                                                    <  4:54120/126‑1 (MQ=255)                                                   caACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGgcgc                                                                                           >  8:222264/1‑149 (MQ=255)                                                    aaCTGGAGACAAACGGGGCGGCATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCt                                                                                          <  7:210853/149‑1 (MQ=255)                                                     aCTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTg                                                                                         <  4:1914/149‑1 (MQ=255)                                                       tGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTc                                                                                       <  7:222264/149‑1 (MQ=255)                                                              aaaCGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGgcg                                                                                            <  7:47591/137‑1 (MQ=255)                                                              aaaCGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGgcg                                                                                            >  8:47591/1‑137 (MQ=255)                                                              aaaCGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGgcg                                                                                >  4:81719/1‑149 (MQ=255)                                                                 cGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCAt                                                                             <  3:15571/149‑1 (MQ=255)                                                                   gggCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATgg                                                                           <  1:50102/149‑1 (MQ=255)                                                                        gTATCGGTACCGGATACCGAACATTCCCATGTGGGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTACCAGACCGCCATCGGCGCt                                                                                          >  1:59105/1‑130 (MQ=255)                                                                        gTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTACCAGACCGCCATCGGCGCt                                                                                          <  2:59105/129‑1 (MQ=255)                                                                         tATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTAt                                                                                                            <  3:81099/110‑1 (MQ=255)                                                                         tATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTAt                                                                                                            >  4:81099/1‑110 (MQ=255)                                                                         tATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCa                                                                     <  5:369786/149‑1 (MQ=255)                                                                             ggTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAg                                                                  <  4:228364/148‑1 (MQ=255)                                                                                aCCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCtt                                                              >  7:86527/1‑149 (MQ=255)                                                                                 ccGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTc                                                             <  3:81719/149‑1 (MQ=255)                                                                                   ggATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTcca                                                           <  3:337472/149‑1 (MQ=255)                                                                                         cGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTccagccag                                                      >  3:168089/1‑148 (MQ=255)                                                                                              aTTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCa                                                >  4:127984/1‑149 (MQ=255)                                                                                                tCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACt                                              >  3:211586/1‑149 (MQ=255)                                                                                                  ccATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCg                                            >  2:306045/1‑149 (MQ=255)                                                                                                          gggCGGAGTCACGGGCATTGAGCCATAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAAGAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAAt                                     >  8:97608/1‑149 (MQ=255)                                                                                                          gggCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCaa                                      <  8:86527/148‑1 (MQ=255)                                                                                                                aGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTtctc                               <  2:153366/149‑1 (MQ=255)                                                                                                                     cGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAAtctt                                  >  2:46624/1‑141 (MQ=255)                                                                                                                     cGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAAtctt                                  <  1:46624/141‑1 (MQ=255)                                                                                                                         cATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTc                      <  4:168089/149‑1 (MQ=255)                                                                                                                          aTTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTcc                     >  6:223440/1‑149 (MQ=255)                                                                                                                                  aaaaGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGTGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATa             >  6:81335/1‑149 (MQ=255)                                                                                                                                    aaGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACt           <  4:211586/149‑1 (MQ=255)                                                                                                                                      tcTTCGCGGGTTCACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCGGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTg         >  4:184403/2‑149 (MQ=255)                                                                                                                                      gCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGTGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTg         <  5:81335/149‑1 (MQ=255)                                                                                                                                      gCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTg         <  2:198167/149‑1 (MQ=255)                                                                                                                                       cTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGc        >  2:315245/1‑149 (MQ=255)                                                                                                                                       cTTCGCGGGGTCACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGc        >  1:106037/1‑149 (MQ=255)                                                                                                                                           gcgGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGCCAGt    >  2:102853/1‑149 (MQ=255)                                                                                                                                             gggTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGCCAGttt  >  5:138155/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                                 AGCTGCGGCGGCGCTGCAACGCGCAGGGGAGTGAATGCGCGATCTTGCAGCAACTGGAGACAAACGGGGCGGTATCGGTACCGGATACCGAACATTCCCATGT‑GGGGCGGAGTCACGGGCATTGAGCCAAAAGCTTCGCGGGTGAACCCGCGAAGAGGTCAGTTCTAACAATAGAGATCTATCAGACCGCCATCGGCGCTGTCATCGGCGCATGGTGCTCATAGCCTTCCAGCCAGAAATCACTCGGCTCAATCTTCTCCAGCCACTCCGGCTCATACTTGCCAGTTT  >  NC_002947/5866553‑5866840

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑