Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006881	3,285,264	(T)7→8	intergenic (‑84/+136)	U712_16905 ← / ← U712_16910	Transcriptional repressor sdpR/Glycine betaine/carnitine/choline transport system permease protein opuCD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	3,285,257	1	.	T	98.4%	216.8 / ‑3.3	63	intergenic (‑77/+143)	U712_16905/U712_16910	Transcriptional repressor sdpR/Glycine betaine/carnitine/choline transport system permease protein opuCD
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (31/31);  total (31/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

AACAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285122‑3285390                                                                                                                                         |                                                                                                                                      aaCAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑ttt                                                                                                                                    >  4:414302/1‑139 (MQ=255)      aTCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑ttttttt                                                                                                                                >  1:50829/1‑138 (MQ=255)            aaTTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTtaaaaac                                                                                                                         <  1:421757/139‑3 (MQ=255)                      cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCaaa                                                                                                                <  7:119659/139‑1 (MQ=255)                            ggATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGt                                                                                                           <  6:154649/138‑1 (MQ=255)                                        gCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAt                                                                                              >  7:103967/1‑139 (MQ=255)                                         cTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAtt                                                                                             >  4:431360/1‑139 (MQ=255)                                         cTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAtt                                                                                             >  6:36358/1‑139 (MQ=255)                                           ttGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAtttt                                                                                           >  3:204915/1‑139 (MQ=255)                                             gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  7:4614/1‑139 (MQ=255)                                             gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  7:421286/1‑139 (MQ=255)                                             gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  6:422479/1‑139 (MQ=255)                                             gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  6:166092/1‑139 (MQ=255)                                                 aCATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAtt                                                                                     <  2:139251/139‑1 (MQ=255)                                                   attattCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAtttt                                                                                   >  1:411645/1‑139 (MQ=255)                                                   attattCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAtttt                                                                                   >  5:417140/1‑139 (MQ=255)                                                   attattCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAtttt                                                                                   >  1:59116/1‑139 (MQ=255)                                                   attattCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAtttt                                                                                   >  1:48881/1‑139 (MQ=255)                                                       ttCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGGTATAATATCTGATTTTTGTATTTTTTCa                                                                               <  7:226721/139‑1 (MQ=255)                                                          aTAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCaaa                                                                             <  8:352603/138‑1 (MQ=255)                                                            aGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATAc                                                                          >  5:368869/1‑139 (MQ=255)                                                             gCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACt                                                                         <  8:378389/139‑1 (MQ=255)                                                             gCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACt                                                                         >  7:151634/1‑139 (MQ=255)                                                             gCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACt                                                                         <  6:145440/139‑1 (MQ=255)                                                               gTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCg                                                                       >  6:5927/1‑139 (MQ=255)                                                                 tttCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     >  7:271195/1‑139 (MQ=255)                                                                 tttCTCCTTAACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAATTTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     >  7:277826/1‑139 (MQ=255)                                                                  ttCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     <  3:198096/138‑1 (MQ=255)                                                                  ttCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACACTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     >  5:164934/1‑138 (MQ=255)                                                                   tctcCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGAt                                                                    <  2:59116/138‑1 (MQ=255)                                                                   tctcCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGAt                                                                    <  3:208686/138‑1 (MQ=255)                                                                          tACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCTGATAATCCCaa                                                            >  3:163936/1‑139 (MQ=255)                                                                                   acatttagacatttagATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGaaa                                                   <  2:50829/139‑1 (MQ=255)                                                                                     atttagacatttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAat                                                 <  4:201355/139‑1 (MQ=255)                                                                                     atttagacatttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAat                                                 <  4:341492/139‑1 (MQ=255)                                                                                          gacatttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGtt                                            <  4:380185/139‑1 (MQ=255)                                                                                             atttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTTTAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         <  7:35624/139‑1 (MQ=255)                                                                                             atttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         <  5:417945/139‑1 (MQ=255)                                                                                             atttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         <  8:271195/139‑1 (MQ=255)                                                                                             atttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         <  8:277826/139‑1 (MQ=255)                                                                                               ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATATTCCAAACGCTGGAAAATATGTTTaa                                         >  1:155258/1‑137 (MQ=255)                                                                                               ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         >  5:392589/1‑137 (MQ=255)                                                                                               ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         >  7:58015/1‑137 (MQ=255)                                                                                               ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         >  3:37865/1‑137 (MQ=255)                                                                                               ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCATCAAATTGGTTATAATATCTTATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGATGGAAAATATGTTTaa                                         >  8:203977/1‑137 (MQ=255)                                                                                                tagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACa                                       <  2:429122/138‑1 (MQ=255)                                                                                                tagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACa                                       <  6:346815/138‑1 (MQ=255)                                                                                                   atatTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  6:115979/139‑1 (MQ=255)                                                                                                    tatTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  4:157734/138‑1 (MQ=255)                                                                                                      tttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACt                                 <  1:423970/138‑1 (MQ=255)                                                                                                       ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGaaa                                                   <  6:18099/119‑1 (MQ=255)                                                                                                       ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGaaa                                                   >  5:18099/1‑119 (MQ=255)                                                                                                       ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               >  1:95231/1‑139 (MQ=255)                                                                                                         gTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAGTACTCGGATAATCCCAACGCTCGAAAATATGTTTAACAGATACTAaca                             >  4:372730/1‑139 (MQ=255)                                                                                                         gTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAac                              <  3:384122/138‑1 (MQ=255)                                                                                                                    ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               >  5:93843/1‑126 (MQ=255)                                                                                                                    ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               <  6:93843/126‑1 (MQ=255)                                                                                                                    ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  7:127611/1‑139 (MQ=255)                                                                                                                           cATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaa            <  8:151634/138‑1 (MQ=255)                                                                                                                            aTTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaa           >  2:265099/1‑138 (MQ=255)                                                                                                                            aTTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaa           >  3:314852/1‑138 (MQ=255)                                                                                                                             ttATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaaaa         <  2:78545/139‑1 (MQ=255)                                                                                                                                taACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAac       <  3:431360/138‑1 (MQ=255)                                                                                                                                  aCTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGTATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAaccac    <  5:166092/139‑1 (MQ=255)                                                                                                                                    ttGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACct  <  5:5927/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                                      AACAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285122‑3285390

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑