Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	3,855,442	T→G	10.3%	pseudogene (1522/1617 nt)	glvC ←	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	3,855,442	0	T	G	10.3%	132.3 / 4.3	53	pseudogene (1522/1617 nt)	glvC	pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component
Reads supporting (aligned to +/- strand):  ref base T (20/27);  new base G (2/4);  total (22/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGGTGCTTCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGCCGACCC  >  CP009273/3855304‑3855588                                                                                                                                           |                                                                                                                                                   aaGGTGCTTCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAAGGATCACCTGa                                                                                                                                          >  2:574738/1‑149 (MQ=255) aaGGTGCTTCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTCAGATACATGCAGAACAAGGaac                                                                                                                                                >  1:117524/1‑141 (MQ=255)        ttCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAAGTAAGCTATCGAGCTGCTCGCGGCGCTGGGATACATGCAGACCAATGATCACCTGAATGGCAt                                                                                                                                   >  2:432804/1‑149 (MQ=255)        ttCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACAGTTTCTGCTGATGGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGaa                                                                                                                                         <  1:56915/143‑1 (MQ=255)         tCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGGTCCCCTGAAt                                                                                                                                        >  1:452997/1‑143 (MQ=255)         tCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAAt                                                                                                                                        <  1:378049/143‑1 (MQ=255)             ccGCCTGCGACAACCACTGAGAATTTGGTCATTATTCTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCa                                                                                                                              <  2:157118/149‑1 (MQ=255)               gCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCCCCTGAATGGCATCGCCACt                                                                                                                            >  2:209894/1‑149 (MQ=255)                  tGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATCAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGcc                                                                                                                               <  1:467126/143‑1 (MQ=255)                     gaaaaCCACTGAGAATTTGGTCATTATACTGCCGCCGTAATGGCAACATTTTCTGCTGATTGATGAGAAGTAATTAATCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGTATggattagcagta                                                                                                                            <  1:210224/140‑11 (MQ=255)                     gACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGaa                                                                                                                      <  2:185488/149‑1 (MQ=255)                     gACAACCACTGAGAATTTGGTCATTATACTGCCTCAGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATAATCACCTGAATGGCATCGCCACTATGGaa                                                                                                                      <  2:386989/149‑1 (MQ=255)                       cAACCACGGAGAATTTGGTAATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGa                                                                                                                    <  2:168448/149‑1 (MQ=255)                         aCCACTGAGAATTTGGTCAGTATACTCCCTCCGTAATAGCAACCTTTTCTGCTGATTGATGAGGATTAATTTAGCTATCGAGCAGTTCACGCAGCTGAGATACAAGCAGACCAATGCTCACCTGAATAGCCTCGCCACTACgg                                                                                                                        >  1:270155/1‑143 (MQ=255)                            aCTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCg                                                                                                               <  2:263534/149‑1 (MQ=255)                              tGAGAATTTGGTCATTATACTGCCTCCGTAAAGAACAGAATATCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCCCCTGAATGGCATCGCCACTACGGACGACGCCGTg                                                                                                             >  2:630713/1‑149 (MQ=255)                               gagaAGTGGGTCATTATACTGCCTCCGTAGTGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAAGGATCACCTGAATGGCATCGCCAATACGGAAGACg                                                                                                                  <  1:119848/143‑1 (MQ=255)                                    tttGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCTGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTcc                                                                                                       <  2:439024/149‑1 (MQ=255)                                       ggTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAg                                                                                                    >  2:97080/1‑149 (MQ=255)                                        gTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGc                                                                                                   >  2:42560/1‑149 (MQ=255)                                                  tGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGa                                                                                         <  2:179235/149‑1 (MQ=255)                                                     cgccGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGTTTTTTaa                                                                                            <  1:387248/141‑1 (MQ=255)                                                     cTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACtt                                                                                      <  2:556495/149‑1 (MQ=255)                                                                cAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGc                                                                           <  2:292295/149‑1 (MQ=255)                                                                 aaCATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCGACTACGGAAGACGCCGTGCGCTCCCGACTGGTGAAATACTTCGtant                                                                                >  1:521390/1‑140 (MQ=255)                                                                   ccttgtcggcggcttgagGGGAATTAATGGAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCGGAATGGCATCGCCACTACGGAAGACGCCGTGCGCCCCCAGCTTTTTAAAGACTTCGTCATCCAGCGtt                                                                        <  2:541002/136‑1 (MQ=255)                                                                   cATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGtt                                                                        <  2:595222/149‑1 (MQ=255)                                                                         ctgctgATTGATGAGAATTAATTAAGCTATCGAGCAGTTTACGCATCTTAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGAc                                                                  <  2:432703/149‑1 (MQ=255)                                                                           gctgATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGCCGCCGTGCGCTCCCAGCTTTTTAAAGCCTTCGTCATCCAGCGGTtg                                                                      >  1:487638/1‑143 (MQ=255)                                                                               tatctccagaATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGAc                                                                  >  1:341153/8‑143 (MQ=255)                                                                                 tgatgaGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAAGGTTCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATg                                                          <  2:131027/149‑1 (MQ=255)                                                                                 tgatgaGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAAGGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATg                                                          <  2:131048/149‑1 (MQ=255)                                                                                   atgaGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCGGCGTTTGTGACATGt                                                              >  1:193270/1‑143 (MQ=255)                                                                                       gaATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAAGGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATg                                                          <  1:518689/143‑1 (MQ=255)                                                                                         attaattaAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCa                                                        <  1:253975/143‑1 (MQ=255)                                                                                                   cTATCGAGCTGGTCCCGCAGCGGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAAcg                                        <  2:146627/149‑1 (MQ=255)                                                                                                    tATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCCATACGt                                             >  1:511484/1‑143 (MQ=255)                                                                                                        gAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTcg                                   >  2:365623/1‑149 (MQ=255)                                                                                                         gtcTGGTCACGAAGCTGAGCTACATGCAGACCAATGATCCCCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAAcg                                        <  1:335963/141‑1 (MQ=255)                                                                                                         aGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCGGCGTTTGTGACATGTCATGCAGTGCAATACTTAAAAGCGTcgc                                  >  2:2732/1‑149 (MQ=255)                                                                                                         aGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGATTGTGACATGTCATGCAGTGCAATACGtcaccc                                        >  1:246602/1‑138 (MQ=255)                                                                                                           cTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGCCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCgcgc                                <  2:306999/149‑1 (MQ=255)                                                                                                              ttCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAAt                             >  2:637026/1‑149 (MQ=255)                                                                                                                 aCGCAGCTGAGATAAATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCACTGCAATACGTAAACGCGTCGCGCAATTGt                          <  2:400238/149‑1 (MQ=255)                                                                                                                        tGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCt                   >  2:182429/1‑149 (MQ=255)                                                                                                                               cATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGata            <  2:384555/149‑1 (MQ=255)                                                                                                                                aTGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTgg                 >  1:181933/1‑143 (MQ=255)                                                                                                                                    aGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGcc       >  2:553241/1‑149 (MQ=255)                                                                                                                                     gACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGata            <  1:86919/143‑1 (MQ=255)                                                                                                                                       ccAATGATCACCTGAATGGCATCGCCACTACGGACGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGCCGAc    <  2:88180/149‑1 (MQ=255)                                                                                                                                        cAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGCCGAcc   >  2:636637/1‑149 (MQ=255)                                                                                                                                        cAATGATCACCTGAACGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTg         <  1:186833/143‑1 (MQ=255)                                                                                                                                         aaTGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGCCGAccc  <  2:396975/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                   AAGGTGCTTCCACCGCCTGCGACAACCACTGAGAATTTGGTCATTATACTGCCTCCGTAATGGCAACATTTTCTGCTGATTGATGAGAATTAATTAAGCTATCGAGCTGTTCACGCAGCTGAGATACATGCAGACCAATGATCACCTGAATGGCATCGCCACTACGGAAGACGCCGTGCGCTCCCAGCTTTTTAAAGACTTCGTCATCCAGCGTTTGTGACATGTCATGCAGTGCAATACGTAAACGCGTCGCGCAATTGTTAATGCTGGAGATATTGCCGACCC  >  CP009273/3855304‑3855588

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑