Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092733,659,0620CA59.3% 13.4 / 40.7 27A37S (GCG→TCG) gadXacid resistance transcriptional activator GadX
Reads supporting (aligned to +/- strand):  ref base C (10/1);  new base A (0/16);  total (10/17)
Fisher's exact test for biased strand distribution p-value = 1.30e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.09e-05
Rejected as consensus: Frequency below/above cutoff threshold.

ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC  >  NZ_CP009273/3658977‑3659138
                                                                                     |                                                                            
aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaa                                                                          >  2:143605/1‑90 (MQ=255)
 tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCaaaaa                                                                         >  1:91932/1‑90 (MQ=255)
           taataaAAGCGTGCCCCTTGACACAAATAAAAATTTTTCAACACACTTATCTACTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCAcc                                                               <  1:143605/90‑1 (MQ=255)
            aatGAAAGCGTGCCCCTTGACACAAATAAAAAATTTTCAACACCTTTATCTCCTCAATTTTGGCTTGCACCCGCAAAACCCAGGTCACCg                                                              <  1:213755/90‑1 (MQ=255)
            aatAAAAGCGTGTCCCTTGACACAAATAAAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCg                                                              <  2:304150/90‑1 (MQ=255)
                     gtgtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa                                                     >  2:181668/1‑90 (MQ=255)
                       gtCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATa                                                   >  1:84830/1‑90 (MQ=255)
                            ttGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat                                              >  2:478709/1‑90 (MQ=255)
                             tGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGata                                             >  1:235762/1‑90 (MQ=255)
                                cacaAATACAAAATTTTCAACACCCTTATCTCCTCGAATTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  2:91932/90‑1 (MQ=255)
                                cacaAATAAAAATTTTTCACCCCATTTATCTCCTCAATTTTGGTTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  2:362010/90‑1 (MQ=255)
                                cacaAATAAAAAATTTTCAACACACTTATCTCCTCGATTTTGGCTTGCATCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  2:209055/90‑1 (MQ=255)
                                cacGAATAAAAATTTTTCAACCCATTTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  2:145181/90‑1 (MQ=255)
                                cacGAATAAAAATTTTTCAACACACTTATCTCCTCGAATTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTc                                          <  2:234355/90‑1 (MQ=255)
                                cacGAAAACAAAATTTTCAACACATTTATCTACTCGAATTTGGCTTGCACCCGAAAAACCCAGGACACCGCCATTAAAATAGCGATATTc                                          <  2:155018/90‑1 (MQ=255)
                                      aaaaaaaTTTCCAACACACTTATCTACTCGATTTTGGCTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCAtt                                    <  1:252592/87‑1 (MQ=255)
                                           aaTTTTCAAACCCTTTATCTACTAAATTTTGGTTTCCACCCAAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCa                               <  1:456754/90‑1 (MQ=255)
                                                  aaCACCCTTATCTCCTCAAATTTGCCTTGCACCCAAAAAAACCAGTCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                        <  1:478709/90‑1 (MQ=255)
                                                  aaCACATTTATTTCCTAAATTTTGGTTGGCACCCGAAAAACCGAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                        <  2:361960/90‑1 (MQ=255)
                                                  aaCACATTTATCTCCCCAATTTTGGCTTCCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag                        <  2:523379/90‑1 (MQ=255)
                                                     ccacTTATCTCCTCAATTTTGTCTTCCACCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat                     <  1:132828/89‑1 (MQ=255)
                                                      cccTTATCTCCTCAATTTTGGCTTCCACCCGAAAAACCCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata                    <  2:2994/88‑1 (MQ=255)
                                                        cTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatata                  >  1:167672/1‑90 (MQ=255)
                                                                  cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt        >  2:340068/1‑90 (MQ=255)
                                                                  cGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCtt        >  2:89349/1‑90 (MQ=255)
                                                                       ttGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATa   >  2:246470/1‑90 (MQ=255)
                                                                        tgccTTCCACCCGAAAAACCCAGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc  <  2:210851/87‑1 (MQ=255)
                                                                                     |                                                                            
ATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACACTTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC  >  NZ_CP009273/3658977‑3659138

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑