Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,796,627	C→T	11.3%	intergenic (‑185/+33)	pvdH ← / ← PP_4224	diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,796,627	0	C	T	11.3%	136.2 / 7.6	53	intergenic (‑185/+33)	pvdH/PP_4224	diaminobutyrate‑2‑oxoglutarate transaminase/sensor histidine kinase
Reads supporting (aligned to +/- strand):  ref base C (20/27);  new base T (3/3);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.18e-01

ACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATCGCCAGC  >  NC_002947/4796481‑4796771                                                                                                                                                   |                                                                                                                                                  aCATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCAc                                                                                                                                                 <  6:118775/149‑1 (MQ=255)   aTGGGTATCTCCTCGAGAGCAAGGGGTTGGGCGGTTTTCGCCTTGGAAACGCTTGAGTGGGGGGAGGATTTATCGGTTGTTACGCGTGTTTATTTTTCTCTGTGCTGGCCTCTTCGCGGGTGAACCCGCTCCTACGGGCGGGTTTAccc                                                                                                                                               <  8:110674/149‑1 (MQ=21)   aTGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCAccc                                                                                                                                               <  5:47929/149‑1 (MQ=255)    tGGGTAAATCCTCGCGAGCAAGCGGATGGGCGTTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAACCCGCTCCTACGGGCGGGTTTACCcg                                                                                                                                              <  5:21023/149‑1 (MQ=37)     gggTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTAGTTAAGCGATTTTATTTTTGTATGTGATGGCCTCTTAGCTGGTAAACCCGCCCGTAGGAGAGGTTTCaaactc                                                                                                                                             >  3:117144/1‑144 (MQ=255)      ggTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCcgc                                                                                                                                             <  8:323116/148‑1 (MQ=255)       gTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCCCCcgcg                                                                                                                                            >  1:140807/1‑148 (MQ=255)          aaTCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAa‑ga                                                                                                                                       <  5:290817/149‑1 (MQ=255)           aTCCTCTCGAGCAATAGGATGGGAGGTTATCGCTTTGGAAAGGGTTGAGTGGGGGGTGGATTTAGGGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAa‑gag                                                                                                                                      <  4:117144/149‑1 (MQ=38)              cTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGc                                                                                                                                    <  1:211560/148‑1 (MQ=255)              cTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGGGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAACCCGCTCCTACGGGCGGGTTTACCCGCGAA‑GAGGc                                                                                                                                    <  7:320713/148‑1 (MQ=25)               tCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCCCCCGCGAA‑GAGGc                                                                                                                                    >  2:230176/1‑147 (MQ=255)                     gCAAGCGGAGGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAg                                                                                                                            <  5:20473/149‑1 (MQ=255)                       aaGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGc                                                                                                                                    >  1:8749/1‑139 (MQ=255)                       aaGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGc                                                                                                                                    <  2:8749/139‑1 (MQ=255)                          cGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGAt                                                                                                                       <  8:179652/149‑1 (MQ=255)                                 gCGGTTATCGCTTTGGAAACGCTTGAGGGGTGGGAGGATTTAGCGGTTGTTCCGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATc                                                                                                                <  8:327400/149‑1 (MQ=255)                                   ggTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCaa                                                                                                              <  4:16622/149‑1 (MQ=255)                                     ttATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATg                                                                                                            >  6:201777/1‑149 (MQ=255)                                        tCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCAGAAGGAGCGGGTTCACACGCGAA‑GAGGCCAGCACATGCGATAAACATCAATgac                                                                                                          >  2:253172/1‑146 (MQ=255)                                        tCGCTTTGGAAACGCTTGAGTGGGGGGAGGATGTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGccc                                                                                                         <  1:139726/149‑1 (MQ=255)                                        tCGCTTTGGAAACGCTTGAGTGAGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTGAACCCGCTCCTACGGGCGGGTTTACCCGCGAA‑GAGGCCAg                                                                                                                                 >  7:233723/1‑125 (MQ=21)                                          gCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAACGAGGCCAGCACAGGCGATAAACATCAATGCCCa                                                                                                        <  1:50209/149‑1 (MQ=255)                                          gCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCa                                                                                                        <  3:63586/148‑1 (MQ=255)                                           cTTTGGAAACGCTTGAGGGGGTGGAGGATTTAGCGTTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGTGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGTA‑GAGGCCAGCACAGGCGATAAACATGAATGCCCAgg                                                                                                      <  1:253172/149‑1 (MQ=39)                                            tttGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGa                                                                                                     >  5:290192/1‑149 (MQ=255)                                            tttGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCCATAAACATAAATTGCCAGGa                                                                                                     >  3:356642/1‑149 (MQ=255)                                                 aaaCGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCAGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACgcgc                                                                                                >  1:56618/1‑149 (MQ=255)                                                  aaCGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGcc                                                                                               >  8:182951/1‑149 (MQ=255)                                                              gggggATGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGcaa                                                                                    <  5:201777/148‑1 (MQ=255)                                                                 ggaggaTTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACACGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGcaacaa                                                                                 >  1:296495/1‑148 (MQ=255)                                                                                 gttACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCAc                                                                >  5:298412/1‑149 (MQ=255)                                                                                    aCGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTa                                                              <  6:290192/148‑1 (MQ=255)                                                                                     cgcgATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCa                                                                                                                                  <  8:252098/79‑1 (MQ=255)                                                                                     cgcgATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCa                                                                                                                                  >  7:252098/1‑79 (MQ=255)                                                                                     cgcgATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACg                                                            <  7:182951/149‑1 (MQ=255)                                                                                     cgcgATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACg                                                            <  2:336973/149‑1 (MQ=255)                                                                                               tttttGTCTGTGCTGGCTTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCGGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCaaa                                                   <  6:30682/148‑1 (MQ=255)                                                                                                 tttGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAgc                                                 <  2:56618/148‑1 (MQ=255)                                                                                                    gTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCa                                              <  2:296495/148‑1 (MQ=255)                                                                                                                  ctTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACAcc                               >  7:325817/1‑149 (MQ=255)                                                                                                                   ttCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCg                              >  6:196703/1‑149 (MQ=255)                                                                                                                          gtgaaCCCGCTCCTACGGGCGGGTTTACCCGCGAA‑GAGGCCAGCACAGACGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCAc                        >  3:293910/4‑148 (MQ=37)                                                                                                                               cccgcccgTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGc                  >  4:164284/1‑149 (MQ=255)                                                                                                                               cccgcccgTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGc                  >  3:119627/1‑149 (MQ=255)                                                                                                                                 cgcccgTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCt                <  6:298412/149‑1 (MQ=255)                                                                                                                                    ccgTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGca             >  4:248112/1‑149 (MQ=255)                                                                                                                                        acgggCGGGTTTACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAAt         >  4:90535/5‑149 (MQ=255)                                                                                                                                         ggAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATc        <  1:230176/149‑1 (MQ=255)                                                                                                                                          gAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATCg       >  3:363014/1‑149 (MQ=255)                                                                                                                                           aGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCACCTGCACAATCGc      <  5:196703/149‑1 (MQ=255)                                                                                                                                            gCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATCGcc     <  2:140807/149‑1 (MQ=255)                                                                                                                                               ggTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATCGCCAGc  >  4:105500/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                  ACATGGGTAAATCCTCGCGAGCAAGCGGATGGGCGGTTATCGCTTTGGAAACGCTTGAGTGGGGGGAGGATTTAGCGGTTGTTACGCGATTTTATTTTTGTCTGTGCTGGCCTCTTCGCGGGTAAACCCGCCCGTAGGAGCGGGTTCACCCGCGAA‑GAGGCCAGCACAGGCGATAAACATCAATGCCCAGGACGCGCCGGTACCTGCAACAAAACCCGCAAGCCGTCACTACGGCTGTCAAAGCGCAGGCTACCGGCACACCGCTGCACGATCGCCTGCACAATCGCCAGC  >  NC_002947/4796481‑4796771

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: ‑