Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,150,023	C→T	11.5%	intergenic (+22/‑375)	PP_3654 → / → PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,150,023	0	C	T	11.5%	130.0 / 7.6	52	intergenic (+22/‑375)	PP_3654/PP_3655	leucine‑responsive regulatory protein/cytosine/purine/uracil/thiamine/allantoin permease family protein
Reads supporting (aligned to +/- strand):  ref base C (15/31);  new base T (3/3);  total (18/34)
Fisher's exact test for biased strand distribution p-value = 4.05e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

GCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAACGCGCACATCGCACCAACCCAGCCCACCGTGATCCGGTTGCCACC  >  NC_002947/4149876‑4150171                                                                                                                                                    |                                                                                                                                                      gCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCC                                                                                                                                                      >  2:335754‑M1/1‑149 (MQ=255)      ggACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGC                                                                                                                                                 <  2:225025‑M1/149‑1 (MQ=255)       gACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCG                                                                                                                                                >  4:331907‑M1/1‑149 (MQ=255)        aCCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGCCCAGTATTCCCAATGTGAAACTCTTGAGCTCGTCCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGG                                                                                                                                               <  2:295858‑M1/149‑1 (MQ=255)        aCCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATCTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGG                                                                                                                                               <  1:335754‑M1/149‑1 (MQ=255)        aCCCGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGG                                                                                                                                               <  3:15547‑M1/149‑1 (MQ=255)         ccTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGG                                                                                                                                              <  7:35‑M1/149‑1 (MQ=255)          cTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGG                                                                                                                                              >  8:220805‑M1/1‑148 (MQ=255)          cTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGG                                                                                                                                              >  7:45072‑M1/1‑148 (MQ=255)             ccGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTA                                                                                                                                            <  7:150932‑M1/147‑1 (MQ=255)              cGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAAC                                                                                                                                         <  5:410035‑M1/149‑1 (MQ=255)                  gTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGC                                                                                                                                     <  1:395656‑M1/149‑1 (MQ=255)                  gTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGC                                                                                                                                     <  3:395521‑M1/149‑1 (MQ=255)                   tttCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGAAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCcgcg                                                                                                                                    >  7:140556/1‑149 (MQ=255)                       aGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAACCGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctg                                                                                                                                >  3:320791‑M1/1‑144 (MQ=255)                        gAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGGGCCGGCCTCTTCGCGGGTAAACCCGCtcctgc                                                                                                                               >  4:249394‑M1/1‑143 (MQ=255)                           gCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATAGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACACGCGCCTGCa                                                                                                                              >  3:50286/1‑147 (MQ=255)                            cTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAg                                                                                                                           <  1:223902/149‑1 (MQ=255)                               tATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctgcgacgggc                                                                                                                        >  4:134908‑M1/1‑136 (MQ=255)                               tATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGt                                                                                                                         <  8:45072/148‑1 (MQ=255)                                 tGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGAc                                                                                                                      <  4:74186/149‑1 (MQ=255)                                 tGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGAc                                                                                                                      <  5:53323/149‑1 (MQ=255)                                   aCGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGt                                                                                                                    <  7:220805/149‑1 (MQ=255)                                      atcACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGTAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTTTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGc                                                                                                                 <  2:309597/147‑1 (MQ=255)                                        cACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCG                                                                                                                                                  <  8:91931‑M1/114‑1 (MQ=255)                                                cAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTACCTCTTGTGCCGGCCTCTTCGCGGGTAAAACCGCtcctgcgacgggctacgtcacctttgcagg                                                                                                       >  7:257820‑M1/1‑119 (MQ=255)                                                  gTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCCCGCCTGCAAAGGTTGCGTATCACGTCGCACGAg                                                                                                     <  7:54490‑M2/149‑2 (MQ=255)                                                   tATTCCGAATGTGAAACGGTTGAGCTCGACCTTGGTGATGAATGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTACCTCTTGTGCCGGCCTCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgc                                                                                                    <  8:257820‑M1/149‑34 (MQ=255)                                                   tATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgc                                                                                                    <  4:320791‑M1/149‑34 (MQ=255)                                                     ttCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGGGCCGGCCTCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcg                                                                                                   <  3:249394‑M1/148‑35 (MQ=255)                                                        ccAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCTCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcgg                                                                                                  >  5:210665‑M1/1‑111 (MQ=255)                                                        ccAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCTCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcgg                                                                                                  <  6:210665‑M1/146‑36 (MQ=255)                                                        ccAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAgcgggtt                                                                                               <  6:176715‑M2/149‑8 (MQ=255)                                                        ccAATGTGAAACGCTTGAGCTCGACCTTGGTGAAGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTGTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAgcgggt                                                                                                >  3:46072‑M2/1‑142 (MQ=255)                                                           aTGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcgggtttac                                                                                            <  3:134908‑M1/149‑42 (MQ=255)                                                           aTGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAgcgggtttac                                                                                            >  8:140556‑M2/1‑139 (MQ=255)                                                             gtgAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTATCCCGTGGCACGAgagggtttaccc                                                                                          <  7:362396‑M2/149‑13 (MQ=255)                                                              tgAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAgcgggtttacccg                                                                                         <  1:263459‑M2/149‑14 (MQ=255)                                                                aaaCGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAgcgggtttacccgc                                                                                        <  6:174007‑M2/148‑15 (MQ=255)                                                                           cTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCCCCTGCAAAGGTGACGTACCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAggccccc                                                                            >  2:94979/1‑146 (MQ=255)                                                                               aCCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcg                                                                                                   <  7:318103‑M1/122‑35 (MQ=255)                                                                               aCCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCtcctgcgacgggctacgtcacctttgcaggcgcg                                                                                                   >  8:318103‑M1/1‑88 (MQ=255)                                                                                        atgaAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCttt                                                               <  5:176715/149‑1 (MQ=255)                                                                                            aggaagTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑c                                                          >  5:297037/1‑149 (MQ=255)                                                                                              gaagTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTg                                                        >  7:105177/1‑149 (MQ=255)                                                                                                          gATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAATGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAAcgc                                            <  4:50286/149‑1 (MQ=255)                                                                                                           aTCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAAcgcg                                           <  7:235472/149‑1 (MQ=255)                                                                                                            tCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAACgcgc                                          <  5:174007/149‑1 (MQ=255)                                                                                                                                    tCCTCTTGTGCCGGCCCCTTCGCGGGTAAAACCGCGCCTGCAAAGGTTACGTAGCCCGTAGCAGGAGCGGGGTTAACCGCGAAGAGGCCGGCCCACGCCACCATTAAA‑CAGCCCAGAAAACCCGCCCCTCCCACCCACACAGCCCACCg                  >  8:27478/1‑149 (MQ=255)                                                                                                                                     ggtctTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAACGCGCACATCGCACCAACCCAGCCCACCGt                 <  2:219570/147‑1 (MQ=255)                                                                                                                                         tggtgCCGGCCCCTTCGGGGGAAACCCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTAACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAACGCGCACATCGCACCAACCCAGCCCACCGTGa               <  3:331907/145‑1 (MQ=255)                                                                                                                                              ccGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCGGTCGCAGGAGGGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCATCCTGCCCTGAAAACGCGCACATCGCACCAACCCAGCCCACCGTGATCCgg          <  1:94979/148‑1 (MQ=255)                                                                                                                                                    ccTTCGCGGGTAAACCCGCGCCTGCAAAGGTGAGGTAGCCCGTCACCGGAGCGGGGTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGGCCAGAAAACGCGCACATCGCACCAACCCAGCCCACCGTGATCCGGTTGCcccc  >  4:381133/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                      GCCAAGGACCTGCCGGCGTTTCAGAAGCTGTATGACGAGCACCTGACCAGTATTCCCAATGTGAAACGCTTGAGCTCGACCTTGGTGATGAAGGAAGTGATCCAGGATCGGTTGCTCCCCATGTAGCTGTTTCCTCTTGTGCCGGCCCCTTCGCGGGTAAACCCGCGCCTGCAAAGGTGACGTAGCCCGTCGCAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAACCTTTCAT‑CTGCCCTGAAAACGCGCACATCGCACCAACCCAGCCCACCGTGATCCGGTTGCCACC  >  NC_002947/4149876‑4150171

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: ‑