Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,157,962:1	+C	100%	coding (58/1833 nt)	PP_4542 →	ABC transporter ATP‑binding protein/permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,157,962	1	.	C	80.0%	119.3 / 27.5	45	coding (58/1833 nt)	PP_4542	ABC transporter ATP‑binding protein/permease
Reads supporting (aligned to +/- strand):  ref base . (7/2);  new base C (16/20);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

AAGTCCGCCAAACGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCAGCCGGATCATC  >  NC_002947/5157819‑5158099                                                                                                                                                 |                                                                                                                                                 aaGTCCGCCAAACGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑c‑‑c‑c‑cc                                                                                                                                        >  3:78368/1‑149 (MQ=255)   gTCCGCCAAACGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑c‑‑c‑c‑cc‑‑cc                                                                                                                                    >  4:198064/1‑149 (MQ=255)        ccAAACGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑c‑‑c‑c‑cc‑‑cccgagc                                                                                                                               >  4:77646/1‑144 (MQ=255)           aaCGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACg                                                                                                                             >  6:79465/1‑149 (MQ=255)                         ctgCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTa                                                                                                               <  2:25107/149‑1 (MQ=255)                            cAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTAc                                                                                                              <  2:265215/147‑1 (MQ=255)                            cAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTAc                                                                                                              <  4:78368/147‑1 (MQ=255)                            cAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCt                                                                                                            >  6:154481/1‑149 (MQ=255)                                     caGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACGGATCGAGTTTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑CGCC‑‑CCGAGCACGGTGGGGCCGGTGTACGGGTAGTAcgt                                                                                                   >  8:131267/1‑147 (MQ=255)                                      aGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTg                                                                                                  <  3:270459/149‑1 (MQ=255)                                        ggATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGCTATTTTCCGCGAGGCACCGAGCGACGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTCTTACCTgct                                                                                                >  6:190888/1‑148 (MQ=255)                                        ggATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTAACGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCCCCGAGCGAAG‑‑C‑‑C‑CACC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACATgag                                                                                                >  6:195322/1‑147 (MQ=255)                                              gAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGgt                                                                                                                           <  5:6318/116‑1 (MQ=255)                                              gAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGgt                                                                                                                           >  6:6318/1‑116 (MQ=255)                                              gAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGgt                                                                                          >  2:72237/1‑149 (MQ=255)                                               aaaCCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGCCC‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGgt                                                                                          <  2:19862/149‑1 (MQ=255)                                                 aCCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGtgtg                                                                                       >  1:195707/1‑149 (MQ=255)                                                 aCCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑CAC‑CC‑‑CCGAGCACGGTGTGGCAGTTGTACCTGTATTACCTGCGCCAGGtgtg                                                                                       >  3:173072/1‑149 (MQ=255)                                                  ccGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTgg                                                                                      <  6:188131/149‑1 (MQ=255)                                                         aGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCt                                                                               <  3:77646/149‑1 (MQ=255)                                                             tCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGCGCACGGTGTGGCCGTTCTACCTGTATTACATGCGCAAGGTGTGGCCCCGCTTCgg                                                                           >  2:301364/1‑148 (MQ=255)                                                             tCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGt                                                                           <  6:187989/149‑1 (MQ=255)                                                                    aaCAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCctgc                                                                   >  8:120030/1‑149 (MQ=255)                                                                     aCAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCctgc                                                                   >  4:260954/1‑149 (MQ=255)                                                                      cAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCctgct                                                                  <  1:301364/149‑1 (MQ=255)                                                                          aGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCCAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCtggtg                                                              <  5:154481/149‑1 (MQ=255)                                                                                 tCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGTcc                                                       >  8:121022/1‑149 (MQ=255)                                                                                      cATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTc                                                  <  2:195707/149‑1 (MQ=255)                                                                                      cATGCTGTACCGCCGGTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGGGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTc                                                  <  3:198064/149‑1 (MQ=255)                                                                                          cTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑CCAC‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCACCTTCGTGGCCATGCTGGTGGTCGGCCTGGTCGcc                                               >  7:169746/1‑149 (MQ=255)                                                                                           tGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTc                                             >  4:182906/1‑149 (MQ=255)                                                                                           tGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCg                                            >  2:99174/1‑149 (MQ=255)                                                                                              aCCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAAGCACCGAGCGAAGCCC‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGc                                           >  1:58554/1‑149 (MQ=255)                                                                                                cgccgTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGa                                        <  5:79465/149‑1 (MQ=255)                                                                                                  ccgTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATc                                      <  1:72237/149‑1 (MQ=255)                                                                                                        cGAAAGTCTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CCCGCCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCGCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAgg                                  <  8:169746/148‑1 (MQ=255)                                                                                                         gAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTgg                               <  3:182906/149‑1 (MQ=255)                                                                                                          aaaGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGc                              >  1:47343/1‑149 (MQ=255)                                                                                                           aaGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGc                              >  7:28329/1‑148 (MQ=255)                                                                                                                 gctCGATATTTTCCGCGAGGCACCGCGCGAAGC‑C‑‑C‑C‑CC‑‑CCGCGCACGGTGTGGCCGGTCTACCGGTCTTCCCTGCGCCAGGGGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTc                       <  5:190888/147‑1 (MQ=255)                                                                                                                  aTCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTc                       <  5:195322/148‑1 (MQ=255)                                                                                                                   tCGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGGCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAg                     <  3:260954/149‑1 (MQ=255)                                                                                                                    cGATATTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGc                    <  8:66762/149‑1 (MQ=255)                                                                                                                      atatTTTCCGCGAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTa                  >  5:180242/1‑149 (MQ=255)                                                                                                                           ttCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCa             <  7:120030/148‑1 (MQ=255)                                                                                                                               gcgAGGCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCAGCCg         >  6:31323/1‑149 (MQ=255)                                                                                                                                   ggCACCGAGCGAAGC‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCAGCCGGat      >  1:212328/1‑148 (MQ=255)                                                                                                                                      aCCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCAGCCGGatcatc  >  6:306706/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                 AAGTCCGCCAAACGTATCGACTGACTGCAGGCTTCACAGGGATGTGAAACCGCCTGAGGGTCGGACGAACAGGAGTGTTGTCGCCCATGCTGTACCGCCGTTTCGAAAGACTGATCGATATTTTCCGCGAGGCACCGAGCGAAG‑‑C‑‑C‑C‑CC‑‑CCGAGCACGGTGTGGCCGTTCTACCTGTATTACCTGCGCCAGGTGTGGCCCAGCTTCGTGGCCCTGCTGGTGGTCGGCCTGGTCGCCTCGCTGATCGAGGTGGCGATGTTCAGCTACCTCAGCCGGATCATC  >  NC_002947/5157819‑5158099

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: ‑