Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_00091329,4960TA34.8% 75.4 / 30.3 46intergenic (+301/‑155)dapB/carA4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
Reads supporting (aligned to +/- strand):  ref base T (28/2);  new base A (0/16);  total (28/18)
Fisher's exact test for biased strand distribution p-value = 1.54e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

TTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAAT  >  NC_000913/29367‑29633
                                                                                                                                 |                                                                                                                                         
ttGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATccc                                                                                                                                 >  1:864118/1‑140 (MQ=255)
   gcccttttttttCTGCTTTTTTTTATTTCATGCAATCTTCTTGCGGCGCAAGCTTTTTCCAGAACAGGTTAGATGTTTTTTTTGTCGCTTAATGCCTAAAAAACATGCATGACCCAAAAAATAATAAAAAAAATCCCGcc                                                                                                                              <  2:804215/134‑1 (MQ=255)
                      tttttATTTCATGAATTTTTCTTGCTGCGAAAGCTTTTCCAAAAACAGGTAAGATGTTTTTTTTGTCGTTTAATCCCTAAAAAACATGCATGACCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAgcg                                                                                                           <  2:903746/140‑1 (MQ=255)
                        ttttttTCATGCATTTTTTTTGCTGCGAAAGCTTTTCCAAAAACGGTTTAGATGTTTTTTTTGTCTTTTAAGCCCTAAAAAACATGCAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGcc                                                                                                         <  2:746721/140‑1 (MQ=255)
                           ttttCATCCATTTTTCTTGCTGCGCAAGCTTTTCCAAAAACAGTTTAGATGTTTTTTTTGTCTCTTATCCCGTGTAAAACATGCATGACCCAAAAAAAAAAAAAAAAATCCCCGCCATTAAGTTGACTTTTAGCGCCCat                                                                                                      <  2:89496/139‑1 (MQ=255)
                                 tGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:89496/1‑140 (MQ=255)
                                 tGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:705104/1‑140 (MQ=255)
                                 tGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:632129/1‑140 (MQ=255)
                                 tGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:251207/1‑140 (MQ=255)
                                 tGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                >  1:212435/1‑140 (MQ=255)
                                    attttttttGCGGCGAAGGCTTTTCCCAAAACGGGTTAAATGTTTTTTTTGTCGTTTAATGCCTAAAAAACATGAAGGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGa                                                                                             <  2:705104/133‑1 (MQ=255)
                                        ttcttGCGGCGCAAGCTTTTTCAAAAACGGTTTAGATTTTTTTTTTGTCTCTTAATGCTTAAAAAACTTGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgc                                                                                         <  2:864118/140‑1 (MQ=255)
                                          cttGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccg                                                                                       >  1:516161/1‑140 (MQ=255)
                                               ggcgcAAGCTTTTCCCAGAAAAGGTTAGATGTTTTTTTTGTCGCTTAATGCTTAAAAAACATGCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGtt                                                                                  <  2:251207/139‑1 (MQ=255)
                                                gcgcAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                 >  1:619770/1‑140 (MQ=255)
                                                 cgcAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                >  1:531222/1‑140 (MQ=255)
                                                  gcAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGc                                                                               >  1:298119/1‑140 (MQ=255)
                                                           ttCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                      >  1:298384/1‑140 (MQ=255)
                                                                 aaCAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGt                                                                >  2:341663/1‑140 (MQ=255)
                                                                    ggtttAGATTTTTTTTTTGTCGTTTAATCCCTGAAAAACATGCAGGAGCCAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                             <  2:516161/137‑1 (MQ=255)
                                                                    gggTAAGATGATTTTTTTGTCGTTTAATCCTTAAAAAACATGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                             <  2:173111/139‑1 (MQ=255)
                                                                      gTTAGATGATTTTTTTGTCGCTTAATGCCTGAAAAACATGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCAATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                           <  1:98949/140‑1 (MQ=255)
                                                                      gTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                           >  2:398517/1‑140 (MQ=255)
                                                                             tttttttttGCCGTTTAATGCCTGAAAAACATGCAGGACCAAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                    <  2:531222/136‑1 (MQ=255)
                                                                              atttttttGTCGTTTAATGCTTGAAAAACATGCATGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCa                                                   <  1:1065268/137‑1 (MQ=255)
                                                                                cTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                 >  1:394107/1‑140 (MQ=255)
                                                                                cTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                                 >  2:995040/1‑140 (MQ=255)
                                                                                  ttttGCCGTTTAATGCTTGAAAAACATGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGa                                               <  1:1045158/140‑1 (MQ=255)
                                                                                     tGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAttt                                            >  2:944427/1‑140 (MQ=255)
                                                                                        cGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                         >  1:441240/1‑140 (MQ=255)
                                                                                         gCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                        >  2:664339/1‑140 (MQ=255)
                                                                                                   taaaaaaCATGCAGGAGCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGACGGTAAGCAGATTTGCATTGATTTACGTCATCATtgtg                              <  2:353251/137‑1 (MQ=255)
                                                                                                           atgcatgAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                      <  1:535686/140‑1 (MQ=255)
                                                                                                           atgcatgACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                      <  2:310801/140‑1 (MQ=255)
                                                                                                           atgaatgaGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                      <  2:298384/140‑1 (MQ=255)
                                                                                                            tgcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAatat                     >  1:988333/1‑140 (MQ=255)
                                                                                                            tgcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAatat                     >  1:304072/1‑140 (MQ=255)
                                                                                                             gcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATg                    >  2:773977/1‑140 (MQ=255)
                                                                                                             gaatgACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATg                    <  2:330383/138‑1 (MQ=255)
                                                                                                               atgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                  >  1:1033986/1‑140 (MQ=255)
                                                                                                               atgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                  >  1:117183/1‑140 (MQ=255)
                                                                                                               atgAGCCAAAAAAAAATAAAAAAAACCCCGCCATTANNTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                  <  2:298119/140‑1 (MQ=255)
                                                                                                                 gAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCaaa                >  1:541747/1‑140 (MQ=255)
                                                                                                                   gCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATa              >  2:860996/1‑140 (MQ=255)
                                                                                                                    ccACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa             >  1:671563/1‑140 (MQ=255)
                                                                                                                      aaaaaaaaaaaaaaaaaaTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag           <  2:671563/138‑1 (MQ=255)
                                                                                                                       caAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagt          >  2:445603/1‑140 (MQ=255)
                                                                                                                       caAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagt          >  1:1012775/1‑140 (MQ=255)
                                                                                                                        aaaaaaaaaaaaaaaaCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg         <  2:619770/140‑1 (MQ=255)
                                                                                                                           ataataTAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagt      <  1:398517/140‑1 (MQ=255)
                                                                                                                             aataTAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAgtgagtga    <  2:117183/140‑1 (MQ=255)
                                                                                                                             aataAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAgtgagtga    <  2:441240/140‑1 (MQ=255)
                                                                                                                               tataAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAAAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat  >  1:284246/1‑140 (MQ=255)
                                                                                                                                 |                                                                                                                                         
TTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAAT  >  NC_000913/29367‑29633

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑