Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,199,645	G→C	9.4%	intergenic (+20/+53)	PP_4579 → / ← PP_4580	LysR family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,199,645	0	G	C	9.4%	154.4 / 7.0	53	intergenic (+20/+53)	PP_4579/PP_4580	LysR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (20/28);  new base C (3/2);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 6.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

CCTTGAGCTGGTGGTGGCGTGGCAGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCTTTCGACCACAAAGGCCAG  >  NC_002947/5199502‑5199787                                                                                                                                                |                                                                                                                                                ccTTGAGCTGGTGGTGGCGTGGCAGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTACCGGcc                                                                                                                                            >  3:339979/1‑149 (MQ=255)  cTTGAGCTGGTGGTGGCGTGGCAGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGccc                                                                                                                                           >  4:219409/1‑149 (MQ=255)      tggtggtggtggCGTGGGAGACCGGGGTGGGGTTTGTCGATGATGTGGGTGGGGTTTGCCGGCATGTGTTGGCGCGGTATGCGCGGTATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCTACAGTCTCCGCCTGTACCGGCCCTTTc                                                                                                                                       <  6:40660/146‑1 (MQ=255)           gtggtggCGTGGCAGACCGGGTTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCggg                                                                                                                                  <  8:34814/149‑1 (MQ=255)           gtggtggCGTGGCAGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCgg                                                                                                                                   <  3:325583/148‑1 (MQ=255)                        aGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGaaa                                                                                                                    <  1:24854/149‑1 (MQ=255)                        aGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGaaa                                                                                                                    <  5:105476/149‑1 (MQ=255)                        aGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGa                                                                                                                      >  4:159868/1‑147 (MQ=255)                         gACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTACCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAg                                                                                                                   <  4:339979/149‑1 (MQ=255)                          aCCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAgg                                                                                                                  <  1:11891/149‑1 (MQ=255)                          aCCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAgg                                                                                                                  <  3:195700/149‑1 (MQ=255)                             ggggTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGcc                                                                                                               >  3:102260/1‑149 (MQ=255)                                ggcggcatGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggt                                                                                                            <  4:129701/142‑1 (MQ=255)                                 tGGCGTGGGGCGAGGCGGTGGTTGGGGTGTGCGGGCCGGTGTGGGCGGGGTATGCGCGGTATGTGGGGGGGCTGGGGAGCGTGGTGGGCTGACCAACTGTCTCCGCCTGTTGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggta                                                                                                           <  4:192230/149‑1 (MQ=25)                                   gCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggtaca                                                                                                         <  3:159868/149‑1 (MQ=255)                                    cGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggtacag                                                                                                        <  3:354608/149‑1 (MQ=255)                                     gTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAt                                                                                                                               <  2:157321/126‑1 (MQ=255)                                     gTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAt                                                                                                                               >  1:157321/1‑126 (MQ=255)                                         gTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggtacaggtaca                                                                                                   <  4:102260/149‑1 (MQ=255)                                              tGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCCCGGGCAT‑GCCCGCCAAAGGGCCGGGACAGGTAcaccag                                                                                               >  4:339064/1‑148 (MQ=255)                                                     gtTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAgc                                                                                       >  7:50392/1‑149 (MQ=255)                                                     gtTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGAGGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAgc                                                                                       <  3:193123/149‑1 (MQ=255)                                                        ggggTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAgcgc                                                                                     <  8:50392/148‑1 (MQ=255)                                                           gTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTACCGGCCCGTTAGCGGGGAA‑GCCCGCGAAACGGCCgctacacgcgga                                                                                                   >  5:242115/1‑125 (MQ=255)                                                                ccGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGctctct                                                                            <  8:40943/149‑1 (MQ=255)                                                                    cAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTca                                                                        <  3:219409/149‑1 (MQ=255)                                                                            ggCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTg                                                                >  5:156087/1‑149 (MQ=255)                                                                            ggCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCAGCGAAAGGGCCGGTACACGGAAAGCAGAGCTTAGCGCCCGCTGACTTTGACCACCCTg                                                                >  6:96296/1‑149 (MQ=255)                                                                               gcgGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGGCCGGAAAGGGTCAGCAGAACGTAGCGCCAGCGCTCGTTGACCCCCCGgcgc                                                             >  2:130953/1‑149 (MQ=37)                                                                                   tATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑TCCCGCGAAAGGGCCggtacaggt                                                                                                      >  7:319642/1‑104 (MQ=255)                                                                                   tATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCggtacaggt                                                                                                      <  8:319642/104‑1 (MQ=255)                                                                                     tGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGccgcccg                                                       >  6:343636/1‑149 (MQ=255)                                                                                        gcgGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGCGCAT‑GCCCGCCTAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCACTATCACCACCCAGCGCcgcccgcc                                                     >  5:92405/1‑148 (MQ=255)                                                                                                  ggtgggCAGCGGATCGTGCTGGTCTGACCAACAGGCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGTATcagc                                           <  7:3606/148‑1 (MQ=255)                                                                                                      ggCAGCGGATCGTGCTGGTCTGACCAACAGGCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATcagccagc                                       <  1:130953/148‑1 (MQ=255)                                                                                                            ggATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCATGGCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCATCGCCGCCCGCCCAGGATCAGCCAGCCAATcg                                 >  1:286175/1‑148 (MQ=255)                                                                                                             gATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCGGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTGACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCCATccc                                >  5:297527/1‑148 (MQ=255)                                                                                                              aTCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCa                                                   <  5:221140/128‑1 (MQ=255)                                                                                                                     tgttCTGACCACCTGTCTCCTCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCTAATGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAAt                                   <  8:309392/134‑1 (MQ=38)                                                                                                                     tGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTAGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAAt                                   >  7:309392/1‑137 (MQ=255)                                                                                                                     tGGTCTGACCAACAGTCTCCGCCAGTAGCGGCCCTTTACCGGGCAG‑CCCCCCGAAACGCCCGGTACACGAACAGCACAACATACCCCCAACGATAATTAACCACCCACACCCGCCCCCCCCAGATCCCCCACCCCATCCCCCGCAACac                       >  4:272157/1‑148 (MQ=255)                                                                                                                       gTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATca                                             <  6:348373/125‑1 (MQ=255)                                                                                                                       gTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATca                                             >  5:348373/1‑125 (MQ=255)                                                                                                                       gTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAgg                      <  3:339064/148‑1 (MQ=255)                                                                                                                        tCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTAGCGGGCAT‑GCCCGCGAAAGGGGCGGTACAGGTACAGCAGGAATTAGCGCCAGCTCTCTTTCAACCACCAGCGCCGCCCCCCCCGGATCCGCCAGCCACTCCCCACCAACACGCt                    >  7:92762/1‑149 (MQ=37)                                                                                                                         cTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAgg                                                 >  7:314829/1‑119 (MQ=255)                                                                                                                         cTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAgg                                                 <  8:314829/119‑1 (MQ=255)                                                                                                                            aCCAACCGTCTCCGCCTGAAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCAGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCttt                  <  8:92762/147‑1 (MQ=255)                                                                                                                            aCCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCTTTc                 <  5:343636/148‑1 (MQ=255)                                                                                                                               aaCAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGGAAGGGCCGGGTCAGGTTCAGCAGAACTTTGCGCCAGCTCTCGTTACCCCACCGGGGCCGCCCGCCCAGGATGAGCCCGCCAATGCCCCTCAACCGGCTTTGGAcc             >  8:174154/1‑149 (MQ=25)                                                                                                                                         gCCTGTAGCGGCCCTTTCGAGGGCAT‑GCCCGCGAATGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCTTTCGACCACAAAGTCCa   <  6:92405/149‑1 (MQ=255)                                                                                                                                          ccTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCTTTCGACCACAAAGGCCAg  <  6:156087/149‑1 (MQ=255)                                                                                                                                          ccTGTACCGGCCCTTTCGCGGGCCT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGCCCTTAGCGCCCGGTCTCTTTCACCCCCCTGCGCCGCCCGCCCAGGATCAGCCAGCCACTCCCCAGCAACCGGCTTTCGACCACACAGGCCAg  >  5:68822/1‑149 (MQ=37)                                                                                                                                                |                                                                                                                                                CCTTGAGCTGGTGGTGGCGTGGCAGACCGGGGTGGCGTTGGTCGATGAGGTGGTTGGGGTTTGCCGGCAGGTGTTGGCGCGGTATGCGCGGGATGTGGGTGGGCAGCGGATCGTGCTGGTCTGACCAACAGTCTCCGCCTGTAGCGGCCCTTTCGCGGGCAT‑GCCCGCGAAAGGGCCGGTACAGGTACAGCAGAACTTAGCGCCAGCTCTCTTTCACCACCCTGCGCCGCCCGCCCAGGATCAGCCAGCCAATCCCCAGCAACAGGCTTTCGACCACAAAGGCCAG  >  NC_002947/5199502‑5199787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑