Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,665,7020CA22.6% 31.3 / 10.7 31A37S (GCG→TCG) gadXDNA‑binding transcriptional dual regulator GadX
Reads supporting (aligned to +/- strand):  ref base C (18/6);  new base A (0/7);  total (18/13)
Fisher's exact test for biased strand distribution p-value = 6.53e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.44e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAGATTAATGCTCTTTTACGTAGCATTTCTGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCAAATTGATTGATAAATAAATTTAAACGAAGCGGGAGAACAGGATGATAATGTGTGATGTTCTA  >  NC_000913/3665455‑3665937
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                           
aaGATTAATGCTCTTTCATGTAGCATTTCTGCCTCGCGAAGCTTCTTATTCTGCGATAGTTGCGCAACTTCCTGAACAACAGGAATATCTCTCCTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGCTTTAATGCATCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAACG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCaa                                                                                                                                                                                                                                           >  2:424213/1‑250 (MQ=255)
   aTTAATGCTCTTTTACGTAGCATTTCTGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAAc                                                                                                                                                                                                                                       >  1:344932/1‑251 (MQ=255)
                  cGTAGCATTTCTGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCAtt                                                                                                                                                                                                                        >  1:256582/1‑251 (MQ=255)
                            cTGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCg                                                                                                                                                                                                               >  2:145458/1‑250 (MQ=255)
                             tGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat                                                                                                                                                                                                             >  2:14594/1‑251 (MQ=255)
                                      aaGATTTTTATTCTGCTATAGTTGCGCAACTTCCTAAAAAACAGAAATATCTCTACTACAGTGATGAACGAGAAATAAAGAAACTTTTTTATGTGCATGAAGATTTAATCCCTCC‑TCCTTGAGCATCGGAAAAAATAAT‑GAAAG‑CTTGTCCCTT‑CACACGAATACAAAATTTTCAA‑CCCTCTTATCTTCTAGATTTTG‑TCTTGCACCCGAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCAt                                                                                                                                                                                                    <  1:316404/251‑1 (MQ=255)
                                       aGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCAtt                                                                                                                                                                                                   >  1:297160/1‑251 (MQ=255)
                                              tATTCTGCGATATTTGCCAAACTTCCTAAAAAACAGAAATATCTCTACTACAGTGATGAACGAGTAATGAAGAATTTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAAAAAAAAT‑AAAAG‑CTTGTCCCTT‑GACACAAATAAAAAATCTTCAA‑CACATTTATCTCCTCAATTTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCAt                                                                                                                                                                                             <  1:138685/250‑1 (MQ=255)
                                                    gagatagttgcgaaaattctaaaaaaaCAGGAATATCCCTATTACAGGGAGAAAAGATAAAAGAAAAAACTTTTTTATGTGCATAAAATTTTAATGCCCCC‑TCCTTGAGCATCGGGAAAAAAAAT‑AAAAG‑CGTGCCCCTG‑GACAAAAAAAAAAAATTTAAAA‑CCCCTTTATCTCCACAAATTTG‑GTTTGCACCCAAAAAAACCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                                                                                                                                                                                       <  2:75979/228‑1 (MQ=255)
                                                         aGTTGCGCAACTTCCTGAAACACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATATCGATATTCACCATTAACCATGGTGAGAatat                                                                                                                                                                                  >  2:233676/1‑250 (MQ=255)
                                                         aGTTGCGAAATTTCATAAAAAAAAGGAATATATCAACAACAGGGATGAAGGAGTAAGGAAAAAATTTTTTAAGGTGAAGAAAGATTAAATGCCTCC‑TCCGGGGGCATGGGGAAAAAAAAG‑AAAAG‑CG‑GTCCCTTTAACACGAATAAAAAATTTAAAA‑CACACTTATCTCCAAAAATTTG‑GTTGGCACCCGAAAAAACAAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat                                                                                                                                                                                  <  1:233676/250‑1 (MQ=255)
                                                           ttGCGCAAATTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAACGATATTCACCATTAACCATGGTGAGCATATAtt                                                                                                                                                                               >  1:162871/1‑251 (MQ=255)
                                                                         gttaatggtaaatttctctcccacAGTGATAAACGAGAATTGAAGAAACTTTTTTATGTGCATGAAATTTTAATCCCTCC‑TCCTGGAGCATCGGAAAAAATAAT‑GAAAG‑CGTGCCCCTT‑GACACGAATACAAATTTTCCAA‑CACACTTACCTCCTCGATTTTG‑GCTTGCACCCGCAAAACCCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAAc                                                                                                                                                                                                <  1:342050/198‑1 (MQ=255)
                                                                         gAAAAACAGGAATATCTCTACTAAAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAACATTTTCAA‑CACACTAATCTACTCGCATTTG‑GCTTGCATCCGCAAAAACAAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTACGTCTTGCATAc                                                                                                                                                                 >  2:436608/1‑251 (MQ=255)
                                                                              aCAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAAt                                                                                                                                                            >  2:423063/1‑251 (MQ=255)
                                                                                                         aCGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCAt                                                                                                                                 >  1:223224/1‑251 (MQ=255)
                                                                                                                  aaaaaaaCTTTTTTATGTGCATAAAGATTTAAT‑CCTCCCTCCTTAAG‑AACCGGAAAAATTATAGAAGG‑CGTGTCCCTT‑GACACAAAAAAAAAATTTCAAA‑CACATTTACCTACTCGAATTTG‑GCTTGCATCCGCAAAACCCAGGTCTCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTTCATAGTTGACtt                                                                                                                        <  1:135059/247‑1 (MQ=255)
                                                                                                                      aaaCTTTTTTATGTGCATGCAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGCATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCCTTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAat                                                                                                                     >  2:20905/1‑250 (MQ=255)
                                                                                                                                      aTGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAC‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGCGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATAtt                                                                                                     >  1:400025/1‑250 (MQ=255)
                                                                                                                                               taacgccccc‑tcttTGATCAGCGGGAAAAATAA‑‑GAAAGGCGTTTCCCTG‑GACACAAAAACAAAATTTCAAA‑CACCTTTATCTTCCCAAATTTG‑GCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttat                                                                                            <  2:344932/242‑1 (MQ=255)
                                                                                                                                                aaTGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCACCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTttatt                                                                                           >  2:94356/1‑250 (MQ=255)
                                                                                                                                                           cctTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCAcg                                                                                >  1:192430/1‑251 (MQ=255)
                                                                                                                                                              tGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCAcgccg                                                                             >  2:89291/1‑251 (MQ=255)
                                                                                                                                                                     ggggAAAAATAAT‑GAAAG‑CGTTCCCCTT‑GCCCCAAATAAAAATTTTTCAA‑CACCCTTATCTACTCAAATTTG‑GTTTGAATCCGAAAAACCCAGGACACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCtt                                                                      <  1:275829/250‑1 (MQ=255)
                                                                                                                                                                      ggaataaaTAAT‑GAAAG‑CGGGTCCCTG‑GACAAAAATAAAAAATTTTCAA‑CTCACTTATCTACACAATTTTG‑GCTTGCCTCCACAAAAACCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTa                                                                     <  1:14594/246‑1 (MQ=255)
                                                                                                                                                                            aataat‑AAAAG‑CTTGTCCCTT‑GACACAAATAAAAAATTTAAAA‑CACACTTACCTTCTCAAATTGG‑TTTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCaa                                                               <  2:30982/251‑1 (MQ=255)
                                                                                                                                                                                      aggggtgtCCATT‑GCCACAAATACAAA‑TTTTCAAACACCTTTATCTACTAGATTGTG‑GTTTACACCCTCAAAACCAAGTTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATGTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCAAattgattg                                                       <  1:210944/247‑1 (MQ=255)
                                                                                                                                                                                                                            acacTTATTTACAC‑AATTTGTGCTTGCAACCGAAAAAACCAGGTCTCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTGATGTAGCACGCCGCCCTCTTAAGTCAAATTGATTGATAAATAAATTTAAACGAAGCGGGAGAACAtgatga                   <  2:297160/251‑1 (MQ=255)
                                                                                                                                                                                                                                    cTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCAAATTGATTGATAAATACATTTAAACGAAGCGGGAGAACAGGATGATAAtgagt           >  2:123434/1‑248 (MQ=255)
                                                                                                                                                                                                                                           aaTTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCAAATTGATTGATAAATAAATTTAAACGAAGCGGGAGAACAGGATGATAATGTGTGATGTTc    >  1:266648/1‑251 (MQ=255)
                                                                                                                                                                                                                                               tgtccttacATCCACAAAAACCAGGGCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTTATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCGCTCTTAAGTCAAATTGATTGATAAATAAATTTAAACGAAGCGGGAGAACAGGATGATAATGTGTGATGTTCTa  <  1:37681/242‑1 (MQ=255)
                                                                                                                                                                                                                                                             |                                                                                                                                                                                                                                           
AAGATTAATGCTCTTTTACGTAGCATTTCTGCATAGCGAAGATTCTTATTCTGCGATAGTTGCGCAACTTCCTGAAAAACAGGAATATCTCTACTACAGTGATGAACGAGTAATGAAGAAACTTTTTTATGTGCATGAAGATTTAATGCCTCC‑TCCTTGAGCATCGGGAGAAATAAT‑GAAAG‑CGTGTCCCTT‑GACACGAATACAAAATTTTCAA‑CACACTTATCTACTCGAATTTG‑GCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATACGCAATTAGACAATTCCCATGTAGTGATTGCATAGTTGACTTAATATTACATAAACATATTACTGTTTATTAATGTAGCACGCCGCCCTCTTAAGTCAAATTGATTGATAAATAAATTTAAACGAAGCGGGAGAACAGGATGATAATGTGTGATGTTCTA  >  NC_000913/3665455‑3665937

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑