Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 3,285,257:1 +T 100% intergenic (‑77/+143) 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
*CP0068813,285,2571.T94.6% 124.1 / ‑1.0 37intergenic (‑77/+143)U712_16905/U712_16910Transcriptional repressor sdpR/Glycine betaine/carnitine/choline transport system permease protein opuCD
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base T (18/17);  total (18/19)
Fisher's exact test for biased strand distribution p-value = 4.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

ATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285127‑3285390
                                                                                                                                   |                                                                                                                                     
aTCCAAAATTTTTCTCCTTTTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑ttttttt                                                                                                                                >  2:56630/1‑138 (MQ=255)
aTCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑ttttttt                                                                                                                                >  7:195674/1‑138 (MQ=255)
   aaaaaTTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTtaaa                                                                                                                            <  2:138567/138‑1 (MQ=255)
          tttCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAaacaac                                                                                                                       <  5:162586/138‑1 (MQ=255)
                cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCaaa                                                                                                                <  4:238193/139‑1 (MQ=255)
                cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCaaa                                                                                                                <  8:13315/139‑1 (MQ=255)
                cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCaaa                                                                                                                <  8:195674/139‑1 (MQ=255)
                             atatAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCATCAAATTGGTTataata                                                                                                    >  5:19956/1‑138 (MQ=255)
                              tataGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATc                                                                                                  <  2:273058/139‑1 (MQ=255)
                                   cTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAtt                                                                                             >  1:44170/1‑139 (MQ=255)
                                   cTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGAtt                                                                                             >  1:271453/1‑139 (MQ=255)
                                             attattCATAGCGTTTTCTCCTTTACAAAAAAAAATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACACCCCTCAAATTGGTTATAATATCTGATTTTTGTAtttt                                                                                   >  2:114852/1‑139 (MQ=255)
                                                 ttCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCa                                                                               <  8:199180/139‑1 (MQ=255)
                                                        cGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTc                                                                        >  6:39265/1‑139 (MQ=255)
                                                           tttCTCCTTTACAAAAAAACATATAGACATTTAGATATTTGTATAAATGTATTATTTACATTATAACTTGAATTTTTTTTAAAAACAAACCTCAAATTGTTTATAATATCTGATTTTTGTATTTTTTCAAATAATctg                                                                      >  4:266905/1‑136 (MQ=255)
                                                             tctcCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGAt                                                                    <  6:126665/138‑1 (MQ=255)
                                                                     aCAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAAc                                                           <  4:205148/138‑1 (MQ=255)
                                                                         aaaaaCATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTg                                                       >  4:61198/1‑139 (MQ=255)
                                                                               atttagacatttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAat                                                 <  2:271453/139‑1 (MQ=255)
                                                                                    gacatttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGt                                             <  4:200491/138‑1 (MQ=255)
                                                                                         ttagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTaa                                         >  5:218567/1‑137 (MQ=255)
                                                                                                tttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACt                                 <  7:147047/138‑1 (MQ=255)
                                                                                                 ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  4:121658/135‑1 (MQ=255)
                                                                                                 ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   >  3:121658/1‑135 (MQ=255)
                                                                                                 ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  2:284770/135‑1 (MQ=255)
                                                                                                 ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   >  1:284770/1‑135 (MQ=255)
                                                                                                 ttGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               >  4:107451/1‑139 (MQ=255)
                                                                                                  tGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               <  1:56630/138‑1 (MQ=255)
                                                                                                            tattatTTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACAtgttgt                     <  4:275395/138‑1 (MQ=255)
                                                                                                              ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACg                                                          <  1:26825/99‑1 (MQ=255)
                                                                                                              ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACg                                                          >  2:26825/1‑99 (MQ=255)
                                                                                                              ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  8:86389/1‑139 (MQ=255)
                                                                                                              ttattTTCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  4:229555/1‑139 (MQ=255)
                                                                                                                 ttttCATTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGtttatt                >  4:223395/1‑138 (MQ=255)
                                                                                                                      aTTATAACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGGTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTACAACATGTTGTTTATTTaaaa           >  3:236474/1‑138 (MQ=255)
                                                                                                                        tataACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaaaaa        >  7:286789/1‑139 (MQ=255)
                                                                                                                        tataACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaaaaa        >  8:208240/1‑139 (MQ=255)
                                                                                                                          taACTTGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAac       <  5:39265/138‑1 (MQ=255)
                                                                                                                              ttGAATTTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACct  <  3:61198/139‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                     
ATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTTAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285127‑3285390

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: ‑