Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,140,444	A→C	7.2%	intergenic (+108/+272)	PP_4524 → / ← PP_4525	sodium‑solute symporter/LysR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,140,444	0	A	C	7.2%	153.8 / 4.8	56	intergenic (+108/+272)	PP_4524/PP_4525	sodium‑solute symporter/LysR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (25/27);  new base C (2/2);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.84e-01

CGCAAGTCAGTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGACAGTGGTTTATT  >  NC_002947/5140304‑5140588                                                                                                                                              |                                                                                                                                                  cgcAAGTCAGTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCtt                                                                                                                                          >  2:775089/1‑150 (MQ=255)  gcAAGTCAGTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCttt                                                                                                                                         <  2:487306/150‑1 (MQ=255)    aaGTCAGTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGt                                                                                                                                       >  1:150972/1‑150 (MQ=255)          gTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTGGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTaa                                                                                                                                 >  1:185420/1‑150 (MQ=255)           tGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAAt                                                                                                                                <  1:775089/150‑1 (MQ=255)                   gTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGCCCCTTGTCGTTAATCAGCGCCg                                                                                                                        >  1:683843/1‑150 (MQ=255)                      aaGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTa                                                                                                                                  <  2:268520/137‑1 (MQ=255)                      aaGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTa                                                                                                                                  >  1:268520/1‑137 (MQ=255)                              cTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGAc                                                                                                             <  2:150972/150‑1 (MQ=255)                                  ctgctgTAGCGGCCCGTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACGC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGttt                                                                                                         <  1:122588/150‑1 (MQ=255)                                   tgctgTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTg                                                                                                        >  2:699298/1‑150 (MQ=255)                                         aCCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTTCACCCGAGT‑GGGTGCAGCGGCCtttttgt                                                                                                                                     <  1:323398/115‑5 (MQ=25)                                         aCCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTTCACCC‑GAGTGGGTGCAGCGGCCtttttgt                                                                                                                                     >  2:323398/1‑111 (MQ=25)                                          ccGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCgctgct                                                                                                 >  2:112984/1‑150 (MQ=255)                                            ggctttttCGCTTGTAGGATCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGctct                                                                                               <  2:643579/145‑1 (MQ=255)                                             gCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGt                                                                                                                                    <  1:583294/112‑1 (MQ=255)                                             gCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGt                                                                                                                                    >  2:583294/1‑112 (MQ=255)                                                cTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTtcat                                                                                           >  1:614689/1‑150 (MQ=255)                                                cTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTtcat                                                                                           >  1:149349/1‑150 (MQ=255)                                                     gCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGAGAAGCGGCCTTTGTCGTTAATCAGCGCCGAACCTGTGGTCGTTTGAAATGATCTtcattggtg                                                                                      >  2:300452/1‑145 (MQ=255)                                                          tAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCCGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGAt                                                                                >  1:355669/1‑150 (MQ=255)                                                                 gggCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCAcc                                                                         <  2:614689/150‑1 (MQ=255)                                                                   gCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCgg                                                                       >  1:134117/1‑150 (MQ=255)                                                                     ttGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCt                                                                     <  2:185420/150‑1 (MQ=255)                                                                     ttGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGATCGCCTTGGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCt                                                                     >  2:585870/1‑150 (MQ=255)                                                                         ccGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCaa                                                                 >  1:523323/1‑150 (MQ=255)                                                                             gAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGggt                                                             >  2:347088/1‑150 (MQ=255)                                                                              aaaGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGggtg                                                            <  2:518234/150‑1 (MQ=255)                                                                                aGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCGCCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGC‑CGTTATGCATTCGGGATCGGCACCGGCTGCAAGggtggt                                                          <  1:585870/150‑1 (MQ=255)                                                                                 gggCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGgtggtg                                                         <  1:347088/150‑1 (MQ=255)                                                                                     tGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGAt                                                     <  1:699298/150‑1 (MQ=255)                                                                                     tGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGAt                                                     >  1:404258/1‑150 (MQ=255)                                                                                         aCAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGc                                                 <  2:149349/150‑1 (MQ=255)                                                                                               aaTAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAgcgc                                                                                                                          <  2:236992/72‑1 (MQ=255)                                                                                               aaTAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAgcgc                                                                                                                          >  1:236992/1‑72 (MQ=255)                                                                                               aaTAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAg                                           >  1:95891/1‑150 (MQ=255)                                                                                               aaTAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAg                                           <  2:488789/150‑1 (MQ=255)                                                                                                 tAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGCCGGCTCAGCCCCAAggg                                         >  2:326142/1‑149 (MQ=255)                                                                                                    aaaTCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGAc                                      >  2:573579/1‑150 (MQ=255)                                                                                                     aagcagcagACACAAAAGGGCCTCTGCACCC‑ACTCGGGTGAAGCGGCGTTTGTCGTTAAAAACCGCTATCGCGGTTGACGTTTGCCCAGCTCGTCAT‑CAGTCGGGATCGGCACCGGCGGCAAGGGTGGTGGGATCAGCCCCAAGGCGACa                                     <  2:134117/147‑1 (MQ=255)                                                                                                          gcagACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAg                                <  2:366876/150‑1 (MQ=255)                                                                                                              acacAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGc                                                                                                                                                <  1:474774/35‑1 (MQ=255)                                                                                                              acacAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGc                                                                                                                                                >  2:474774/1‑35 (MQ=255)                                                                                                                acaAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATg                          <  1:101804/150‑1 (MQ=255)                                                                                                                acaAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATg                          <  1:573579/150‑1 (MQ=255)                                                                                                                 caAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATgg                         <  2:523323/150‑1 (MQ=255)                                                                                                                  aaaaaGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTCAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGa                        >  2:578888/1‑150 (MQ=255)                                                                                                                    aaaGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGc                      <  2:470777/150‑1 (MQ=255)                                                                                                                      aGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCa                    <  1:112984/150‑1 (MQ=255)                                                                                                                       ggCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAg                   <  2:95891/150‑1 (MQ=255)                                                                                                                             tGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGAc             >  2:276720/1‑150 (MQ=255)                                                                                                                                     gagtgggTGCAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGACAGTGGtt      >  1:576608/5‑150 (MQ=255)                                                                                                                                     attCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGGGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGACAGTGGtt      <  2:355669/148‑1 (MQ=255)                                                                                                                                      cTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAgg                                                               >  2:214153/1‑92 (MQ=255)                                                                                                                                      cTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAgg                                                               <  1:214153/92‑1 (MQ=255)                                                                                                                                         gggTGCAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGACAGTGGTTTAtt  <  2:576608/150‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                  CGCAAGTCAGTGGCGGCGGTGAAGCTGGCCTGACTGCTGTACCGGCCCTTTCGCTTGTAGGAGCGGGCTTGCCCGCGAAAGGGCTGGTACAGGCAATAGAAATCAGCAGACACAAAAAGGCCGCTGCACCC‑ACTCGGGTGAAGCGGCCTTTGTCGTTAATCAGCGCCGACGCGGTTGACGTTTGCGCTGCTCTTCAT‑CAGTCGGGATCGGCACCGGCTGCAAGGGTGGTGGGATCAGCCCCAAGGCGACAGCCAGGTCATGGAGCCAGTTTGACAGTGGTTTATT  >  NC_002947/5140304‑5140588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑