Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,628,625	0	A	C	22.4%	120.8 / 11.1	49	V105G (GTC→GGC)	pdeF	cyclic di‑GMP phosphodiesterase PdeF
Reads supporting (aligned to +/- strand):  ref base A (36/2);  new base C (0/11);  total (36/13)
Fisher's exact test for biased strand distribution p-value = 2.68e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAG  >  NC_000913/2628486‑2628756                                                                                                                                               |                                                                                                                                    gCTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGa                                                                                                                                     <  2:752866/140‑1 (MQ=255)  cTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGAc                                                                                                                                    >  2:247464/1‑140 (MQ=255)  cTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGAc                                                                                                                                    >  1:164049/1‑140 (MQ=255)                tACAAATGCAGAAAACTGAAAAAG‑TATCAGAAACAGCGTTGCAGAAAACACAATCTGCAAGAATATCCGCGGGAAAATAAAACGGGTATCCCCATGTAAAAC‑GTTGTTC‑CGCGGGGGAGAAAAGCCCCTGAAACCGcccc                                                                                                                      <  2:1623558/140‑1 (MQ=255)                  cAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCaa                                                                                                                    >  1:625262/1‑140 (MQ=255)                  cAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCaa                                                                                                                    >  1:1019767/1‑140 (MQ=255)                    aaTGCAGAAAACTGAAAAAG‑TATCAGAAACAGCGTTGCAGAAAACACAATCGGCCAGAATATACGCGGGAAAATAAAACGGGTATCACCATGTAAAAC‑GTTGTTA‑CGCCGGGGAGAAAAGCCCCTGTAACCGCCCCAACa                                                                                                                  <  2:134516/140‑1 (MQ=255)                         agcaAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaa                                                                                                             >  1:68980/1‑140 (MQ=255)                         agcaAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaa                                                                                                             >  1:653450/1‑140 (MQ=255)                         agcaAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaa                                                                                                             >  1:54161/1‑140 (MQ=255)                          aaaaaCTGAAAAAG‑TATCAAAAACAGCGTTGCAGAAAACACAATCTCCAAAAATATCCGCTGGAAAATAAAACGGGTATCCCCATGTAAAAC‑GTTGTTA‑CGCGGGGGAGAAAAGCCCCTGAAACCGCCCCAACAGAGaat                                                                                                            <  2:1880556/138‑1 (MQ=255)                             aattgaaaaaG‑TATAAAAAACAGCGTGGAAGAAAACAAAATCTGCAAGAATATACGCTGGAAAATAAAACGGGTATCCCCAGGTGAACC‑TTTGTTC‑CGCGGGGGATAAAAGCCCCTGAAACCGCCCCAACAGAGaatgat                                                                                                         <  2:1118884/134‑1 (MQ=255)                                tGGAAAAG‑TATCAAAAACAGCGTTGAAGAAAACACAATCTGCAAGAATATAGGCGGGGAAATTAACGGGGTATCCCCATGTAAACG‑GTTGTTG‑CGCGGGGGAGTAAAGCCCCTGTAACCGCCCCAACAGAGaatgataat                                                                                                      <  2:718574/140‑1 (MQ=255)                                gtgAAAAGTTATAAGAAACAGGGTTGCAGAAACCACAATCTGCAAGAATATACGCGGGAAAATAAAAGGGGTACCCCCATGTGAAAG‑TTTGTTA‑CGCGGGGGAGAAAAGCCCCTGTACCCGCCCCAACAGAGaatgataa                                                                                                       <  2:1506175/138‑1 (MQ=255)                                     aaG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGaatgataactgtct                                                                                                 >  1:428374/1‑134 (MQ=255)                                           tCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATaaaa                                                                                            >  1:2022675/1‑140 (MQ=255)                                               aaaCAGGGTTGCAAAAAACAAATTCCGCCAAAATATCCGCTGGAAAATAAACCGGTTCTCCCCATGTGAACG‑GTGTTTA‑CGCGGGGGAGAAAACCCCTTGAATCCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                        <  2:1019767/140‑1 (MQ=255)                                               aaaCAGCGTTGCAGGAAACCCAATCTGCCAGAATATACGCGGGAAAATAAAACGGTTACCCCCATGTAAAAC‑TTTGTTA‑CGCCGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                        <  2:54161/140‑1 (MQ=255)                                               aaaCAGCGTTGCAGAAAACACAATCTGCAAAAATATACGCGGGAAAATAAAACGGGTACCCCCATGTAAAAC‑TTTTTTC‑CGCCGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                        <  2:625262/140‑1 (MQ=255)                                               aaaCAGCGTTGCAGAAAACAAAATCTCCAAAAATATACGCGGGGAAATAAAACGGGTATCCCCATGTAAAAC‑GTTGTTA‑CGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAg                                                                                        <  2:68980/140‑1 (MQ=255)                                                   aGCGTTGCAGGAAACACAATCTGCCAGATTATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGt                                                                                    >  2:691051/1‑140 (MQ=255)                                                     cGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTa                                                                                  >  1:1543817/1‑140 (MQ=255)                                                     cGTTGCAAGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCTGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTa                                                                                  >  1:701644/1‑140 (MQ=255)                                                         gCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGa                                                                              >  1:1646923/1‑140 (MQ=255)                                                         gCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGa                                                                              >  1:1460924/1‑140 (MQ=255)                                                          cAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGAt                                                                             >  1:1061306/1‑140 (MQ=255)                                                           agaaaaCACAATCTCCAAAAATATACGCGGGGAAATAAAACGGGTATCACCATGTAAAAC‑TTTGTTA‑CGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATa                                                                            <  2:697919/137‑1 (MQ=255)                                                               aaCACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGt                                                                        >  2:176412/1‑140 (MQ=255)                                                                  acaATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTc                                                                     >  1:370928/1‑140 (MQ=255)                                                                    attCTGCCAGAAGATAGGGTGGGAAATTAAAGGGGTATCACCA‑GTCAAACGGTTGTCC‑CGCCGGGGATTAACACCCGAGAACCCGCCCCAACAGAGAATGATAATGCTAATAAAATTAGCCGTTAATGATAGCGTTTCGt                                                                   <  2:1224051/138‑1 (MQ=255)                                                                      ttggcaaGAATATACGTTGGGAATTTAATCGGAAATCTCCATGAG‑ACT‑GTTGGGATGGCGGGGGAGAAAATCCCTTATCACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaa                                                                 <  2:1382259/134‑1 (MQ=255)                                                                      tCTGCCAGAATATACGCGGGAAAATAAAACGGGTATCACCATGAAAAAC‑TTTGTTA‑CGCGGGGGAAAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaa                                                                 <  2:540888/140‑1 (MQ=255)                                                                       cTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaaa                                                                >  1:1382259/1‑140 (MQ=255)                                                                       cTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTaaa                                                                >  2:1587826/1‑140 (MQ=255)                                                                                 ataCGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGctc                                                      >  2:1370137/1‑140 (MQ=255)                                                                                         ggAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATAtt                                              >  1:1211191/1‑140 (MQ=255)                                                                                          gAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATAttt                                             >  2:81182/1‑140 (MQ=255)                                                                                             ataaagggggTACCCCCATGTAAACT‑TTTGTTC‑CGCGGGGGAGAAAACCCCTTGAAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCg                                          <  2:506986/133‑1 (MQ=255)                                                                                              ttAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCgg                                         >  1:971138/1‑140 (MQ=255)                                                                                                   ggggTATCACCATGTGAAAC‑TTTGTTA‑CGCGGGGGAGAAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACaaa                                    <  2:1646923/139‑1 (MQ=255)                                                                                                      gTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATGAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAAt                                 >  2:1795788/1‑140 (MQ=255)                                                                                                          cACCATGTAAAAC‑TTTGTTC‑CGCGGGGGAGAAAACCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCt                             <  2:971138/140‑1 (MQ=255)                                                                                                              aTGTGAAAC‑GTTGTTA‑CGCGGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATGAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAgg                         <  1:1795788/140‑1 (MQ=255)                                                                                                                gtgAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                       >  1:953877/1‑140 (MQ=255)                                                                                                                gtgAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                       >  1:532752/1‑140 (MQ=255)                                                                                                                gtgAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                       >  2:640714/1‑140 (MQ=255)                                                                                                                gtgAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCg                       >  2:1496805/1‑140 (MQ=255)                                                                                                                 tgAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGa                      >  1:1633304/1‑140 (MQ=255)                                                                                                                    aaC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATcc                   >  2:568019/1‑140 (MQ=255)                                                                                                                    aaC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATcc                   >  1:1198429/1‑140 (MQ=255)                                                                                                                        gttgttA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTg                >  2:1061823/1‑140 (MQ=255)                                                                                                                              a‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATg          >  2:1480927/1‑140 (MQ=255)                                                                                                                                cGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAGAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATgc         >  2:1423949/1‑140 (MQ=255)                                                                                                                                  ccGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATgccg       >  1:936681/1‑140 (MQ=255)                                                                                                                                     gggAGTAAAGCCCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc    <  2:1043963/140‑1 (MQ=255)                                                                                                                                     gggAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGccc    >  2:1783611/1‑140 (MQ=255)                                                                                                                                       gagaAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAg  <  1:176412/140‑1 (MQ=255)                                                                                                                                               |                                                                                                                                    GCTCGCCAGTAATCCTACAAATGCAGCAAACTGGAAAAG‑TATCAGAAACAGCGTTGCAGGAAACACAATCTGCCAGAATATACGCTGGGAAATTAAACGGGTATCACCATGTGAAAC‑GTTGTTA‑CGCCGGGGAGTAAAGACCCTGTAACCGCCCCAACAGAGAATGATAATGATAATAAAATTAGCCGTTAATGATAGCGTTTCGTAAAAACCCAGCTCTGCATATTTGCGGACAAAAATCCCTAAGGCGATCCCTGGCAATGCCGCCCAG  >  NC_000913/2628486‑2628756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑