Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,560,362 G→A intergenic (+496/+260) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,560,3620GA91.3% 61.2 / ‑1.3 24intergenic (+496/+260)rtcR/glpGDNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (11/10);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.66e-01

CTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTC  >  NC_000913/3560121‑3560603
                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  
cTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGct                                                                                                                                                                                                                                           >  1:19204/1‑251 (MQ=255)
                   gTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGt                                                                                                                                                                                                                        <  1:221115/251‑1 (MQ=255)
                      gCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGCTGCGCTCTTTTTCTTCGGTCTGGGTGGc                                                                                                                                                                                                                     >  1:273739/1‑251 (MQ=255)
                         ccGCCAATGTCCCCGCCACCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCtt                                                                                                                                                                                                                  <  2:61853/250‑1 (MQ=255)
                            ccAATGATCCCGCCATCGCGGCTGAGTAATTCGCCACCGGCGAGACTGATGCGAAAATCTTCTTTTAACATCACCGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCTGGCGTGGTGCGGATATCGATAAACAGCGTCGCGCCATTGGGG‑ATTTGATCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGATCTGGGTGGCCTTGCg                                                                                                                                                                                                               >  2:176888/1‑251 (MQ=255)
                            caaatgcccccGCCATCTCGGCTGCGTAATTCGCCACCGGCTATAATGATGCGAAAATCTTCTTTTACCATCAAC‑TGTTTTGCAACGTTGAGTTTTTTGTTCACAATGCGCAAATTTCTGTGATTGATCAGTGCTTTCGCTACCGCTTCCGGCGTGGTGCCTATATCGATAAACAGCTTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTg                                                                                                                                                                                                                 <  2:218048/241‑1 (MQ=255)
                             cAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGTGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCgg                                                                                                                                                                                                              >  2:60236/1‑250 (MQ=255)
                                    cccGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGcc                                                                                                                                                                                                       <  1:78170/251‑1 (MQ=255)
                                                              cACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGCAGGc                                                                                                                                                                             >  1:245870/1‑251 (MQ=255)
                                                                                           tttACCAACAACGTGTTA‑GCAACGTGGAGATTGTTGGTGACAATGCGCAAATTGCTGTGAGTGAGCAGTGCGTGCGCTACCGCTTCCGGGGGGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGcgcag                                                                                                                                                   <  1:60236/248‑5 (MQ=255)
                                                                                                   cAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGtttt                                                                                                                                        >  1:131009/1‑251 (MQ=255)
                                                                                                                            gttgGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGCTCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGttgg                                                                                                                >  2:136907/1‑248 (MQ=255)
                                                                                                                                                         tGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGCTGGCGCAGGATCAGGTTTGTCTCCGCCGGCTCATTGAGGGGGCTGCGAATAGTCTGCGGGCTGACGGAGaa                                                                                    >  2:75778/1‑250 (MQ=255)
                                                                                                                                                              aGTGCGTGCGCTACCGCTTCCGGCGTGGGGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGCTCAGGTTTTGCTCAGCCAGCTCAGTGGGGTATCGGCGAAAAGTTTGCGGGCTTGCGGAGAACTGcgc                                                                              >  2:157873/1‑249 (MQ=255)
                                                                                                                                                                       gcTACCGTTTCCGGGGTGGGGCCGATATCTATAAACGGGGGCGAGC‑ATTGGGGGTTTTGCTCCGCCCCTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGAGCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGctc                                                                     <  1:136907/251‑1 (MQ=255)
                                                                                                                                                                                  gggCGTGGTCCCGATATCGATAAACAGGGTCGGCCCATTGGGG‑TTTTGCCCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCTCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGa                                                          <  1:176888/250‑1 (MQ=255)
                                                                                                                                                                                                 atCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt                                           >  1:288692/1‑251 (MQ=255)
                                                                                                                                                                                                 atCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGtt                                           >  1:80014/1‑251 (MQ=255)
                                                                                                                                                                                                       aaccAGCGTCGAGCCATGGGGG‑TTTTGCTCCGCCACTTTGCGGCCGATGCGCTTTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTACCCGACCTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                                     <  1:230570/248‑1 (MQ=255)
                                                                                                                                                                                                                            g‑ATTTGCTCCGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGAc                <  1:26140/251‑1 (MQ=255)
                                                                                                                                                                                                                                 tcccccGCCACTTTGCGGACGATGCGCCCTTTTTCTTCGGTCTGGGTGGCCTTTCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCCCCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGtt             <  1:130977/246‑1 (MQ=255)
                                                                                                                                                                                                                                     ccGCCACTTTGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGATACTGACATACCCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGtgtt        >  2:58142/1‑251 (MQ=255)
                                                                                                                                                                                                                                      cGCCATTTTGCGGACGATGCGCTCTTTTTCTTCGGTTGGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGtgttt       <  1:208113/251‑1 (MQ=255)
                                                                                                                                                                                                                                             ttGCGGACGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCGGGCGGGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTc  <  1:76270/249‑1 (MQ=255)
                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                                  
CTGGGAGATAAAATCGAGCGTCGCTTCGCCAATGATCCCGCCATCGCGGCTGCGTAATTCGCCACCGGCGAGAATGATGCGAAAATCTTCTTTTACCATCAACGTGTTA‑GCAACGTTGAGATTGTTGGTGACAATGCGCAAATTGCTGTGATTGAGCAGTGCGTGCGCTACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGCGTCGAGCCATTGGGG‑ATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTTTGTTTC  >  NC_000913/3560121‑3560603

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑