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.T85.0% 114.6 / 15.1 40intergenic (‑77/+143)U712_16905/U712_16910Transcriptional repressor sdpR/Glycine betaine/carnitine/choline transport system permease protein opuCD
Reads supporting (aligned to +/- strand):  ref base . (2/4);  new base T (18/16);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 6.61e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

TTAACAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285120‑3285390
                                                                                                                                          |                                                                                                                                      
ttAACAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑t                                                                                                                                       >  5:312507/1‑139 (MQ=255)
       aTCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACACAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTGGAA‑tttttt‑tt                                                                                                                               >  2:340906/1‑138 (MQ=255)
       aTCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAATTGTATTATTTTCATTATAACTTGAA‑tttttt‑t                                                                                                                                >  3:13404/1‑138 (MQ=255)
       aTCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTAATTATAACTTGAA‑tttttt‑t                                                                                                                                >  7:84105/1‑138 (MQ=255)
                       cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCaaa                                                                                                                <  8:347497/139‑1 (MQ=255)
                       cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCaaa                                                                                                                <  6:312507/139‑1 (MQ=255)
                       cTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCaaa                                                                                                                <  1:36858/138‑1 (MQ=255)
                         tgttgGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAAtt                                                                                                              >  7:296680/1‑139 (MQ=255)
                                            ttGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGAtttt                                                                                           >  8:133825/1‑139 (MQ=255)
                                            ttGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGAttttt                                                                                          >  4:151840/1‑139 (MQ=255)
                                              gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  1:268656/1‑139 (MQ=255)
                                              gAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTg                                                                                         >  4:70809/1‑139 (MQ=255)
                                                    attattCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTAttttt                                                                                  >  1:66292/1‑139 (MQ=255)
                                                       attCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTc                                                                                <  3:151840/138‑1 (MQ=255)
                                                        ttCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTc                                                                                <  7:133825/138‑1 (MQ=255)
                                                             aGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATAc                                                                          >  2:46538/1‑139 (MQ=255)
                                                             aGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATAc                                                                          >  5:37003/1‑139 (MQ=255)
                                                              gCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATAc                                                                          <  4:13404/138‑1 (MQ=255)
                                                              gCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACt                                                                         <  8:324566/139‑1 (MQ=255)
                                                              gCGTTTTCTCCTTTACAAAAAAACAATTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACt                                                                         <  1:308800/139‑1 (MQ=255)
                                                              gCGTTTTCTCCTTTACAAAAAAACAATTAGACATTTAGATATATGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTTATAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATAc                                                                          <  7:265255/138‑1 (MQ=255)
                                                                  tttCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     >  6:30829/1‑139 (MQ=255)
                                                                   ttCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGa                                                                     >  3:340450/1‑138 (MQ=255)
                                                                    tctcCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGAt                                                                    <  8:294905/138‑1 (MQ=255)
                                                                    tctcCTTTAAAAAAAAAAATTTATACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGAt                                                                    <  1:314823/138‑1 (MQ=255)
                                                                            aCAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCaa                                                            <  1:90947/138‑1 (MQ=255)
                                                                                  aaaCATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTgg                                                      >  2:127770/1‑138 (MQ=255)
                                                                                      atttagacatgtagaTATTTGTATAAATGTAATATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGATATAATATCTGATTATTGTATTTTTTCAAATACTCGGATAATCCCAACGCTCGAAAat                                                 <  8:233434/139‑1 (MQ=255)
                                                                                                 tagaTATTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACa                                       <  3:37777/138‑1 (MQ=255)
                                                                                                    atatTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  6:88323/139‑1 (MQ=255)
                                                                                                    atatTTGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATa                                   <  4:340450/139‑1 (MQ=255)
                                                                                                         tGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACACCCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGG‑AAATATGTTTAACAGATACTAaca                             >  7:165446/1‑139 (MQ=255)
                                                                                                         tGTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaa                               >  1:85556/1‑138 (MQ=255)
                                                                                                          gTATAAATGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTaat                              <  6:37003/138‑2 (MQ=255)
                                                                                                                aTGTATTATTTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACAtgtt                       >  1:139072/1‑139 (MQ=255)
                                                                                                                     ttattTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  8:68002/1‑139 (MQ=255)
                                                                                                                     ttattTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  6:85693/1‑139 (MQ=255)
                                                                                                                     ttattTTCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGttta                  >  5:26119/1‑139 (MQ=255)
                                                                                                                          ttCATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGtttattta              >  8:88436/1‑138 (MQ=255)
                                                                                                                            cATTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATTTTTTACAGATACTAACACATGTTGTTTATTTaaa            <  1:340906/138‑1 (MQ=255)
                                                                                                                             aTTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaa           >  7:289467/1‑138 (MQ=255)
                                                                                                                             aTTATAACTTGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTaaaa           >  7:214549/1‑138 (MQ=255)
                                                                                                                                   aCTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAaccac    <  2:66292/138‑1 (MQ=255)
                                                                                                                                     ttGAATTTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACct  <  6:26119/139‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                      
TTAACAAATCCAAAATTTTTCTCCTTGTTGGATCTGATATAGCTTTGAAAACATTATTCATAGCGTTTTCTCCTTTACAAAAAAACATTTAGACATTTAGATATTTGTATAAATGTATTATTTTCATTATAACTTGAA‑TTTTTT‑TAAAAACAACCCTCAAATTGGTTATAATATCTGATTTTTGTATTTTTTCAAATACTCGGATAATCCCAACGCTGGAAAATATGTTTAACAGATACTAACACATGTTGTTTATTTAAAAAAACCACCT  >  CP006881/3285120‑3285390

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: ‑