Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,534,767	A→C	10.3%	intergenic (+54/‑101)	atoB → / → PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,534,767	0	A	C	10.3%	160.7 / 8.6	59	intergenic (+54/‑101)	atoB/PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter
Reads supporting (aligned to +/- strand):  ref base A (21/30);  new base C (3/3);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 6.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.83e-01

GAGACCGCGCCTGGGGTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCT  >  NC_002947/3534621‑3534904                                                                                                                                                    |                                                                                                                                          gagaCCGCGCCTGGGGTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACa                                                                                                                                         >  3:125439/1‑149 (MQ=255)   gaCCGCGCCTGGGGTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACAtt                                                                                                                                       >  2:47308/1‑149 (MQ=255)            tGGGGTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGAccgccg                                                                                                                               >  5:103074/1‑148 (MQ=255)              gggTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGAGCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCTAATGCGTCGGTACATTGACcgccgc                                                                                                                              <  1:304698/147‑1 (MQ=255)                 tCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGAGCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCGTGAC‑GTGATCGGCCCGTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGGGCGTTGAccgccggctgcg                                                                                                                         >  4:42860/1‑143 (MQ=255)                   aGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGGCGGTCAATGTACCGACGCATTcgcg                                                                                                                       <  1:53582/149‑1 (MQ=38)                   aGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGGCGGTCAATGTACCGACGCATTcgc                                                                                                                        <  2:156948/148‑1 (MQ=38)                    gCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCgg                                                                                                                      >  6:4312/1‑149 (MQ=255)                    gCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCgg                                                                                                                      <  2:195049/149‑1 (MQ=255)                      gTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGt                                                                                                                    <  5:4312/149‑1 (MQ=255)                              actcatcGAGAAAACCGCCCGCCAACTGATCGGGCCGGATGATGGGAAGGAAAAGACCTGCTAAGGCACGAC‑GTGATCTCCCCCTGTAGGCGCGGGATTACCCGCGAAGGCGTCGGTACATAGACCGCCGCATTCGCGGGTAAGCCTGt                                                                                                            <  3:42860/147‑1 (MQ=255)                              aataatCGAGAAAACCGCCGGCAAACTGTTCGTGCCGGATTATTTGAAGGAAATTACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTATGCGGGGGTTTACCCGCGAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAAcccgc                                                                                                            <  4:148500/149‑4 (MQ=21)                              aaTCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGt                                                                                                            <  4:69436/149‑1 (MQ=255)                                   tcGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTa                                                                                                       >  8:33017/1‑149 (MQ=255)                                   tcGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTa                                                                                                       <  5:62714/149‑1 (MQ=255)                                      agaAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAg                                                                                                    >  4:269445/1‑149 (MQ=255)                                      agaAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAg                                                                                                    <  6:103074/149‑1 (MQ=255)                                      agaAAACCGCCGGCAAACTGATCGGGCCGGATTATTTTAAGGAAATTACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAg                                                                                                    <  4:190024/149‑1 (MQ=38)                                              gccgGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGtttttgc                                                                                            <  1:47308/149‑3 (MQ=255)                                              gccgGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTg                                                                                            <  1:185103/149‑1 (MQ=255)                                                     aaCTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGcc                                                                                     <  1:100872/149‑1 (MQ=255)                                                          aTCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGc                                                                                 >  4:247281/1‑148 (MQ=255)                                                                    atgatgTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCtt                                                                       >  1:63947/1‑148 (MQ=255)                                                                    atgatgTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTc                                                                      <  2:347808/149‑1 (MQ=255)                                                                          tgAAGGAAATGACCTTCTAAGGCATGACGGTGATATCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATcc                                                                  >  1:28490/1‑148 (MQ=255)                                                                           gAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCa                                                                >  8:300686/1‑148 (MQ=255)                                                                               gAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATaaaa                                                           >  2:59866/1‑149 (MQ=255)                                                                               gAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATaaaa                                                           >  7:197166/1‑149 (MQ=255)                                                                                aaaTGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAAc                                                          <  4:125439/149‑1 (MQ=255)                                                                                   tGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGc                                                                                 >  3:229836/1‑123 (MQ=255)                                                                                   tGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGc                                                                                 <  4:229836/123‑1 (MQ=255)                                                                                   tGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCaa                                                       >  7:247393/1‑149 (MQ=255)                                                                                        ttCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGAACGCCGCATTCGCCGGTAAGCCAGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCAAAAAACCAATaa                                                    >  6:225057/1‑147 (MQ=255)                                                                                          cTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCt                                                                                                        >  1:121570/1‑93 (MQ=255)                                                                                          cTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCt                                                                                                        <  2:121570/93‑1 (MQ=255)                                                                                          cTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATaaaa                                                  <  7:33017/147‑1 (MQ=255)                                                                                          cTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAg                                                 >  5:206720/1‑148 (MQ=255)                                                                                             aGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAAc                                                          <  1:347407/136‑1 (MQ=255)                                                                                             aGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAAc                                                          >  2:347407/1‑136 (MQ=255)                                                                                             aGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAgg                                                <  3:247281/146‑1 (MQ=255)                                                                                             aGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGaa                                              <  3:269445/148‑1 (MQ=255)                                                                                               gCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCt                                                                                                        >  8:294287/1‑88 (MQ=255)                                                                                               gCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCt                                                                                                        <  7:294287/88‑1 (MQ=255)                                                                                                  tGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAAc                                        <  7:327108/149‑1 (MQ=255)                                                                                                    aC‑GTGATCTCACCCTGTAGGCTCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAAcc                                       <  4:153525/148‑1 (MQ=255)                                                                                                                          gcgGGTTTACCCGCGAATGCGTCGGTTAATTGAACGCCGCATTAGCGGGTAAGCCTGTTGCTAAAGGTTTTTTGCGTTGCCTGGCAATa                                                                             >  8:53103/1‑89 (MQ=25)                                                                                                                          gcgGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATa                                                                             <  7:53103/89‑1 (MQ=255)                                                                                                                            gggTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGc               <  7:300686/149‑1 (MQ=255)                                                                                                                            gggTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGc               <  8:247393/149‑1 (MQ=255)                                                                                                                            gggTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGc               <  6:206720/149‑1 (MQ=255)                                                                                                                                  aCCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAgg                                                >  7:174036/1‑110 (MQ=255)                                                                                                                                  aCCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAgg                                                <  8:174036/110‑1 (MQ=255)                                                                                                                                    ccGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGaa                                              <  6:252482/110‑1 (MQ=255)                                                                                                                                    ccGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGaa                                              >  5:252482/1‑110 (MQ=255)                                                                                                                                      gcgAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcgc     >  5:264269/1‑149 (MQ=38)                                                                                                                                      gcgAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAACCCGCGCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcgc     >  7:311188/1‑149 (MQ=25)                                                                                                                                      gcgAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAACCCGCGCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAAAAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcgc     >  2:263812/1‑149 (MQ=25)                                                                                                                                        gAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCgcgcgc   <  2:28490/149‑1 (MQ=255)                                                                                                                                         aaTGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCt  <  8:197166/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                          GAGACCGCGCCTGGGGTCAGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGAC‑GTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCT  >  NC_002947/3534621‑3534904

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: ‑