Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,560,4551.G97.8% 138.8 / ‑2.6 46pseudogene (151/758 nt)glpRDNA‑binding transcriptional repressor GlpR
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (21/24);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.73e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACG  >  NC_000913/3560318‑3560590
                                                                                                                                          |                                                                                                                                         
tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGcgcagg                                                                                                                                       <  1:745455/143‑6 (MQ=255)
tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCAGCACCGCCATGATGGcgcagg                                                                                                                                       >  1:470301/1‑138 (MQ=255)
            aGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGc                                                                                                                           <  1:1260023/143‑1 (MQ=255)
               cgttGGGGTTTTGGCCCGCCACTTTGCGGGGGTTGCGGTTTTGTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCTCCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTcc                                                                                                                        <  2:319776/141‑1 (MQ=255)
                aTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGCACAGGTTTTGCTCCg                                                                                                                       >  2:861372/1‑143 (MQ=255)
                 ttGGGGAGTTGCTCCGGCACTGCGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGGGCCACGGCGTGTTAACCGAACTGGAAGGCCGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑c                                                                                                                     <  1:1188276/143‑1 (MQ=255)
                    gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAg                                                                                                                  >  1:1253683/1‑143 (MQ=255)
                    gggATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAg                                                                                                                  >  1:573509/1‑143 (MQ=255)
                          tGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCAtt                                                                                                           <  1:344650/143‑1 (MQ=255)
                             tCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGATCCG‑CCAG‑CTCATTGAg                                                                                                        >  1:438814/1‑143 (MQ=255)
                              ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAgg                                                                                                       >  1:482440/1‑143 (MQ=255)
                                     ttgctgggCGTTCCGCTCTTTTTCGTCGGCCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCGGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCgcggc                                                                                                <  1:337295/138‑1 (MQ=255)
                                       ggCGGGCGATGCGCTCTTTTTCGTCGGTCTGGGGGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGa                                                                                              <  1:682128/142‑1 (MQ=255)
                                            gCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGt                                                                                         >  1:606000/1‑143 (MQ=255)
                                              taTGCGCTCTTTTTCTTCTGTCTGGGTGGCCTTGCTATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTACTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCt                                                                                       <  2:388538/142‑1 (MQ=255)
                                                tGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGACTAGGCTGc                                                                                     >  2:349579/1‑143 (MQ=255)
                                                 gcgcTCGGTTTTGTCGGTGTGGGTGGCCTTGCGAGCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCg                                                                                    <  2:423344/143‑1 (MQ=255)
                                                   gcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                                  <  2:573509/143‑1 (MQ=255)
                                                   gcTCTTTTTCTTCGGTCTGGGTGGCCTGGCGCTCCGGCCACCGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑GCTG‑CTCATTCAACTCGCGGCGAATAGTCTGCggg                                                                                  <  2:1253683/143‑1 (MQ=255)
                                                     tcgttctcttcGGTCTGGGTGGCCGTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCt                                                                                <  1:1238273/137‑1 (MQ=255)
                                                          ttcttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGCGGTCGCGGCGAATAGTCTGCGGGCTGACgg                                                                           >  1:453166/1‑143 (MQ=255)
                                                             ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGCCGCGGCGACTAGTCTGCGGGCTGCCGgcga                                                                        >  2:571111/1‑143 (MQ=255)
                                                                  tCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCCTTGAGGTCGCGGCGAATAGCCTGCGGGCTGACGGCGAAATGc                                                                   >  2:1077643/1‑143 (MQ=255)
                                                                  tCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGCCGCGGCGAATAGTCTGCGGGCTGACGgagacaagc                                                                   >  1:1090567/1‑138 (MQ=255)
                                                                   cggggCGGCCTCGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                  <  1:451251/141‑1 (MQ=255)
                                                                   ccggggggCCTTGCGATCGTGCCGCGGCGTGTTAGCCCAACATGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGct                                                                  <  2:563411/141‑1 (MQ=255)
                                                                       gTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGCTGGCGCGGGTTCAGGTTTTGCTCCG‑CCAG‑CTCATTGCGGCCGCGGCGAACGGTCTGCGGCCTGACGGCGCCATGctctcc                                                              >  2:965646/1‑141 (MQ=255)
                                                                       gTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                              <  2:1019427/143‑1 (MQ=255)
                                                                                   tcttGCCACGGCGTGTTAACCGAACTTGTAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGt                                                  <  1:638832/140‑1 (MQ=255)
                                                                                      tGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑GCTTAT‑TGATTTTTCACAAAAGTGACTCACGGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACt                                               >  1:296132/1‑143 (MQ=255)
                                                                                         cACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTCGTGCTCCA‑CCAC‑CCCCTTGAGGGCGAGGCGAATAGCCTGCGCGCCGGCGGCCAAACGCACTACCACCAATTCCGTAcggcc                                            >  2:1152829/1‑139 (MQ=255)
                                                                                               gtgtTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAAcc                                      <  1:197710/143‑1 (MQ=255)
                                                                                                    cgccGAACTGTAAGGCAGCGCCGCACCGCCTTGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCAGTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                                 <  2:792668/141‑1 (MQ=255)
                                                                                                       cGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAGATGCTCTACCAGCTCTTCGGTACTGACATAACCCTCCTGtt                              >  2:1027753/1‑143 (MQ=255)
                                                                                                        gAACTGGAAGGCAGCGCAGCACCGCAATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGTTCGCTGCGAACCGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGttt                             <  1:117836/143‑1 (MQ=255)
                                                                                                            tGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGATGGTTGAca                         >  1:443796/1‑142 (MQ=255)
                                                                                                               aaGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGt                      <  2:747758/143‑1 (MQ=255)
                                                                                                                aGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCCGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGCTTAAccggct                     >  2:96784/1‑139 (MQ=255)
                                                                                                                 ggCAGCGCCGCACCGCCATGATGGCGCCGCATCAGGGTGTGCCCCG‑CCAG‑CTCATCGAGGTCGCGGCCAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACCTAACCCTGCTGTTTAACCAGTTc                    >  2:326814/1‑143 (MQ=255)
                                                                                                                    aGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTGACCAGTGCGat                 >  1:467905/1‑143 (MQ=255)
                                                                                                                    aGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGat                 <  1:1102174/143‑1 (MQ=255)
                                                                                                                     gcgcCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGata                <  1:987252/143‑1 (MQ=255)
                                                                                                                       gccgcACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                  <  2:1017511/139‑1 (MQ=255)
                                                                                                                       gccgcACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                  >  1:1017511/1‑139 (MQ=255)
                                                                                                                        ccgcACCGCCAGGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCAGTGAGGTCGCGGCGAATAGTCTGGGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGataata             <  2:510168/143‑1 (MQ=255)
                                                                                                                          gcACCGCCGTGATGGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCACTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTTACCAGTTCGATAATAcg           >  2:11624/1‑142 (MQ=255)
                                                                                                                                  atgatgGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAc   >  1:719042/1‑143 (MQ=255)
                                                                                                                                   tgatgGCGCAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACg  <  1:1216674/143‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                         
TAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCG‑CCAG‑CTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACG  >  NC_000913/3560318‑3560590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑