Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092735,1590GA37.5% 45.1 / 11.8 32intergenic (+139/‑75)thrC/yaaXthreonine synthase/DUF2502 domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base G (19/1);  new base A (0/12);  total (19/13)
Fisher's exact test for biased strand distribution p-value = 5.76e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGG  >  NZ_CP009273/5028‑5291
                                                                                                                                   |                                                                                                                                    
tCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaac                                                                                                                                >  1:241629/1‑138 (MQ=255)
                gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATc                                                                                                                >  2:810542/1‑138 (MQ=255)
                gCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATc                                                                                                                >  1:542700/1‑138 (MQ=255)
                    ggTTTGTTTTTATGCAGCCCGGTTTTTTTATAAAGAAATTATGGAAAAAAATGACGGGAAAAAAGGAAAAATTCAAAAAAAGGGCGGTAACTTAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAGTa                                                                                                           <  1:537631/139‑1 (MQ=255)
                    ggTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGt                                                                                                            >  1:954302/1‑138 (MQ=255)
                    ggTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGt                                                                                                            >  1:880110/1‑138 (MQ=255)
                    ggTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGt                                                                                                            >  1:71540/1‑138 (MQ=255)
                          tttttATGCAGCCAGGTTTTTTTATAAAAAAATTATGGAAAAAAATGACGGGGAAAAAGGAAAAATTCTCAATAAATGCGTTAACTAAGAGATTAGGATTGCGGAAAAAACCAACCGCCGTTCTCATCGAGCAAtctc                                                                                                      <  1:204340/137‑1 (MQ=255)
                          cTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTcc                                                                                                     >  1:493724/1‑139 (MQ=255)
                               aTGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGata                                                                                                >  2:287247/1‑139 (MQ=255)
                                tGCAGCCGGGTTTTTTTAAAAAAAAATTAGGAAAAAAAATAAAAGGAAAAAAGAAAAAATTCAAAAAAATGGCGTTAACTAAGAGATTAGGATTGAGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                               <  2:493724/139‑1 (MQ=255)
                                    gCCCGGTTTTTTTAAGAAAAAATTAGGAAAAAAAATAACAGGAAAAAAGGAAAAATCCTAAAAAAAGGCGGTAATTAAGAGATTAGGATTGGGGAAAAAAACAGCCGCCGTTCTCATCGAGTAATCTCCGGATATCGAc                                                                                           <  2:602540/139‑1 (MQ=255)
                                     cctggCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  2:923194/4‑139 (MQ=255)
                                     cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  2:938581/1‑139 (MQ=255)
                                     cccGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                          >  1:891522/1‑139 (MQ=255)
                                                 aaaaaaaaaTTAGGAAAAAAAAAAAAAGGAAAAAAGGAAAAATTCAAAAAAAATGGGGTAACTAAGAGATTAGGATGGGGAAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCa                                                                               <  2:891522/132‑1 (MQ=255)
                                                    aagaaATTATGGAGAAACATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGa                                                                           >  2:705516/1‑139 (MQ=255)
                                                                              aaaaaaGAAGAAATTCCAAATAAAGGCGGTAACTAAGAGATGAGGATTGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGAt                                                 <  1:535238/138‑1 (MQ=255)
                                                                                   aGGAAAAATCCACAAAAAGTGCGGTATCTAAAAGTTAAGGATTGCGAAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAAt                                            <  2:241629/139‑1 (MQ=255)
                                                                                         aaTTCTAAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCg                                      <  1:287247/139‑1 (MQ=255)
                                                                                                        acagaaCTAAGAGATAAGTATTGGGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                       <  2:15757/135‑1 (MQ=255)
                                                                                                          ttAACTTAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAGt                                                                                                            <  2:36391/51‑1 (MQ=255)
                                                                                                          gTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGt                                                                                                            >  1:36391/1‑52 (MQ=255)
                                                                                                              cTTAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGTTGCAATCTATCGTACTCGCACTTTCCCTGGTTc                 <  1:93400/139‑1 (MQ=255)
                                                                                                                tAGAGATTATGATTGCGAAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACG‑‑‑‑‑‑‑‑‑‑‑‑‑GGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATg   <  2:954302/138‑1 (MQ=255)
                                                                                                                     aTTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGc          >  2:473409/1‑139 (MQ=255)
                                                                                                                       tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTcctgt        >  1:15757/1‑135 (MQ=255)
                                                                                                                       tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTcctgt        >  1:43026/1‑135 (MQ=255)
                                                                                                                       tAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTc        >  1:849999/1‑139 (MQ=255)
                                                                                                                        aGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTcc       >  1:254542/1‑139 (MQ=255)
                                                                                                                         ggATTGCGAAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTcc       <  2:880110/138‑1 (MQ=255)
                                                                                                                               cGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATgg  >  1:637535/1‑137 (MQ=255)
                                                                                                                                   |                                                                                                                                    
TCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGG  >  NZ_CP009273/5028‑5291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑