Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP025268 2,997,537 (A)8→7 intergenic (‑140/+83) CXP41_RS15625 ← / ← CXP41_RS24400 response regulator transcription factor/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0252682,997,5300A.93.3% 55.4 / ‑1.6 15intergenic (‑133/+90)CXP41_RS15625/CXP41_RS24400response regulator transcription factor/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base . (6/8);  minor base T (0/1);  total (6/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTC  >  NZ_CP025268/2997410‑2997628
                                                                                                                        |                                                                                                  
aGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAAAAAAATTTTGGCGT‑AAAAAAATACCACAGGCAtt                                                                                >  2:1412703/1‑140 (MQ=255)
            ttAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATTAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATga                                                                    >  2:989684/1‑140 (MQ=255)
             tAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATgag                                                                   <  1:1118751/140‑1 (MQ=255)
                          tataATCATACCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAATAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAatat                                                      <  2:6401599/140‑1 (MQ=255)
                                catcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAAt                                                <  1:1218447/140‑1 (MQ=255)
                                 atcCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTATAAATAAAATTTTTGCGT‑AAAAAAATTCCACAGGCAGGAAAAAAGCATGAGATGATTAAAATATTACAAtg                                               >  2:8046828/1‑139 (MQ=255)
                                      ttCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGAtt                                          <  2:3125522/140‑1 (MQ=255)
                                                   ataAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCAt                             <  1:9222663/140‑1 (MQ=255)
                                                                 aaGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAg               <  2:3708938/140‑1 (MQ=255)
                                                                   taaaaCATTTATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGC‑TTAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg             <  2:7208989/136‑1 (MQ=255)
                                                                   gAATACATTTATGAAATAATAATGAAATATAATTAAAAAAAAAATTTTTGAGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg             <  2:7209125/140‑1 (MQ=255)
                                                                   gAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAggg             <  2:1808003/140‑1 (MQ=255)
                                                                       aCATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAgct         >  1:1090371/1‑138 (MQ=255)
                                                                              tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAATTc  >  2:2007087/1‑140 (MQ=255)
                                                                              tgaAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTc  >  2:2007151/1‑140 (MQ=255)
                                                                                                                        |                                                                                                  
AGTGTAAATGCTTTAACGCATTCATTTATAATCATCCCTTCCATTATTATTATAAGCAAAATCCAAAGAATACATTGATGAAATAATAATGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTC  >  NZ_CP025268/2997410‑2997628

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑