Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,735,139	Δ1 bp	7.8%	coding (36/3093 nt)	PP_3302 →	RND family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,735,139	0	A	.	7.8%	156.9 / 7.8	51	coding (36/3093 nt)	PP_3302	RND family transporter
Reads supporting (aligned to +/- strand):  ref base A (27/20);  new base . (2/2);  total (29/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

GAGTGACCTGCACGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGATTATCACTGCCTGGCCCGGCGCCA  >  NC_002947/3734993‑3735281                                                                                                                                                    |                                                                                                                                                gagTGACCTGCACGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGt                                                                                                                                               <  4:140884/149‑1 (MQ=255)    tGACCTGCACGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAc‑g                                                                                                                                           >  6:367782/1‑149 (MQ=255)       ccTGCACGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGTCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑gcga                                                                                                                                        <  4:350594/149‑1 (MQ=255)             cGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACCAAACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGat                                                                                                                                   <  1:92220/149‑1 (MQ=255)                tGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGatcaat                                                                                                                               >  5:139561/1‑149 (MQ=255)                    gatcggatcgTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATTGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGC‑GTACTgcgagcgc                                                                                                                                    <  6:218579/140‑2 (MQ=255)                    gatcggatcgTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGC‑GTACTgcgagcgc                                                                                                                                    >  5:218579/1‑139 (MQ=255)                     atcggatcgTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCAccc                                                                                                                          >  3:299237/1‑149 (MQ=255)                           tcgTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTcc                                                                                                                    >  4:67781/1‑149 (MQ=255)                             gTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCt                                                                                                                   >  2:35431/1‑148 (MQ=255)                                  aCTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATtgt                                                                                                             >  8:249051/1‑149 (MQ=255)                                   cTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATtgtg                                                                                                            <  1:272462/149‑1 (MQ=255)                                    tGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGc                                                                                                           >  7:134226/1‑149 (MQ=255)                                       gTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGa                                                                                                        <  6:139561/149‑1 (MQ=255)                                              tCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCtt                                                                                                 >  3:23386/1‑149 (MQ=255)                                                 gctgcGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATAAGACAGCTGCGTATCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGc                                                                                              >  5:259174/1‑149 (MQ=255)                                                  ctgcGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTc                                                                                                <  4:299237/146‑1 (MQ=255)                                                     cgcgATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCg                                                                                            <  3:67781/147‑1 (MQ=255)                                                          tGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCt                                                                                     >  8:267013/1‑149 (MQ=255)                                                            gCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTgg                                                                                   >  8:29358/1‑149 (MQ=255)                                                                  aGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCtttt                                                                             >  7:80746/1‑149 (MQ=255)                                                                     tCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCa                                                                          <  4:23386/149‑1 (MQ=255)                                                                     tCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCATCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTc                                                                           >  6:51719/1‑148 (MQ=255)                                                                           aaCAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTgg                                                                    <  8:134226/149‑1 (MQ=255)                                                                              aGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATtg                                                                                                              <  6:130589/104‑1 (MQ=255)                                                                              aGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATtg                                                                                                              >  5:130589/1‑104 (MQ=255)                                                                              aGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGcc                                                                 <  7:29358/149‑1 (MQ=255)                                                                                gCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGt                                                               >  2:304636/1‑149 (MQ=255)                                                                                 cTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTg                                                              <  1:370791/149‑1 (MQ=255)                                                                                    aaaCAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTg                                                              >  8:261316/1‑146 (MQ=255)                                                                                    aaaCAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTg                                                              >  2:341940/1‑146 (MQ=255)                                                                                      aCAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCagaa                                                         <  8:80746/149‑1 (MQ=255)                                                                                             aGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTgg                                                                    >  1:80471/1‑131 (MQ=255)                                                                                             aGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTgg                                                                    <  2:80471/131‑1 (MQ=255)                                                                                             aGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATcc                                                    <  5:367782/147‑1 (MQ=255)                                                                                               gTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGccc                                                >  2:211601/1‑149 (MQ=255)                                                                                               gTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGccc                                                <  1:35431/149‑1 (MQ=255)                                                                                                           c‑aaccaTGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAg                                    >  4:241611/1‑149 (MQ=255)                                                                                                           c‑aaccaTGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAg                                    >  8:7754/1‑149 (MQ=255)                                                                                                                caTGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGa                                <  7:249051/149‑1 (MQ=255)                                                                                                                    aGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGa                             <  5:51719/148‑1 (MQ=255)                                                                                                                      ccAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGa                          >  2:363319/1‑149 (MQ=255)                                                                                                                       cAGCTGCGTTTCAACTTATCCGCGCTCGCATTAC‑GCGTGCGATCAATCACCCTATTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGa                          <  1:253118/148‑1 (MQ=255)                                                                                                                        aGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGAt                         >  6:149507/1‑148 (MQ=255)                                                                                                                                 tCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGATTATCACTGcc               >  3:270399/1‑149 (MQ=255)                                                                                                                                   aaCTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGATTATCACTGCCTg             >  4:303136/1‑149 (MQ=255)                                                                                                                                            tcgcTCGC‑GTACTGCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGa                             >  8:173247/2‑124 (MQ=255)                                                                                                                                            tcgcTCGC‑GTACTGCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGa                             <  7:173247/123‑1 (MQ=255)                                                                                                                                            gcgcTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGa                          <  3:268478/127‑1 (MQ=255)                                                                                                                                            gcgcTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGa                          >  4:268478/1‑127 (MQ=255)                                                                                                                                              gcTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGATTATCACTGCCTGGCCCGGCGCCa  >  8:111445/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                GAGTGACCTGCACGCTGGCGATCGGATCGTGGCACTGGGTGCGCATCTGCTGCGCGATGGCGTCGAGGTCATGGAACAGGCTCAAACAGCTCAGGTCATGGGGCACC‑AACCATGAGCCAGCTGCGTTTCAACTTATCCGCGCTCGCAGTAC‑GCGAGCGATCAATCACCCTCTTCCTGATTGTGCTGATCGCCTTCGCCGGCACGCTGGCCTTTTTCAAGCTGGGCCGTGCAGAAGATCCGCCCTTCACCGTCAAGCAGATGACGATTATCACTGCCTGGCCCGGCGCCA  >  NC_002947/3734993‑3735281

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: ‑