Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,862	0	C	A	41.9%	74.0 / 20.6	43	S55R (AGC→AGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base C (18/7);  new base A (0/18);  total (18/25)
Fisher's exact test for biased strand distribution p-value = 8.66e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGA  >  NC_000913/1755716‑1756008                                                                                                                                                   |                                                                                                                                                   gTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCaaa                                                                                                                                                 <  2:618017/150‑1 (MQ=255)      cACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGt                                                                                                                                           >  1:340819/1‑151 (MQ=255)      cACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGt                                                                                                                                           <  2:386219/151‑1 (MQ=255)        ccATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTa                                                                                                                                          >  2:399628/1‑150 (MQ=255)            cGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAc                                                                                                                                      <  2:805028/150‑1 (MQ=255)            cGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAc                                                                                                                                      <  2:796030/150‑1 (MQ=255)              gACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAAccgc                                                                                                                                   <  2:648411/151‑1 (MQ=255)                     aaCCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATc                                                                                                                            >  2:122193/1‑151 (MQ=255)                            tcggAAGAGATGTTAGATAAAATGCTGGCCGTTGGCATGAACGTTATGTGTTTGACCTTCTCTCAGGGTGACAATGCAAAACAGGGTCAGCCCATTCAAATTCTGCCAAAGGTGAAGAGAAAAACGGAAAAAACCGCCGCTATCCTGCtt                                                                                                                      <  1:157142/147‑1 (MQ=255)                                aaGAGTTTTTAGCAAAAATGCGGGCCGCTGGCAAGAACGTTAGGCTTCTGAACTTCCCTCAGGGTGACTATGAAAAACACGGCCAGCGCTTACAAAACCTGCGAAAGGGGATGAGAAAAACGGGAAAAACCGCCGCTATCCTGCTTGAt                                                                                                                   <  2:615900/149‑1 (MQ=255)                                        ttAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTc                                                                                                         >  1:75592/1‑151 (MQ=255)                                         tAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTcc                                                                                                        >  1:593612/1‑151 (MQ=255)                                           gCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCgg                                                                                                      >  1:414378/1‑151 (MQ=255)                                              aaatgggtggcggcgggCATGAACGTTAGGCGTCTAACCTTCTCTCAGGGTGACTATGCAGAACAGGGTCGGCGATTTCAGAATCGGCGCACGGTGAGGAGAAAAACTGATAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGaa                                                                                                    <  2:701563/135‑1 (MQ=255)                                               aaaTGCGGGACGCTGGCATGAACTTTAGGCGTCTAACCTTCTCTCGGGGTGACTAGGAAAAACGGGGTCAGCGCTTTCAAAATCGGCCAAAGGTGATGAAAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAAt                                                                                                  <  2:54080/151‑1 (MQ=255)                                                 aTGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATcc                                                                                                >  2:501817/1‑151 (MQ=255)                                                      ggccgcggccATGAACGTTATGCGTTTGAACTTCTCTCATGGTGACTATGCAGAACCCGGTCAGCGCTTTCAAAATCTGCGAAACGTAATAAGCAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCa                                                                                             <  1:600588/140‑1 (MQ=255)                                                                aTGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTgg                                                                                 >  2:474043/1‑151 (MQ=255)                                                                 tgacctttATCCTTCTGACTTTCTCTCATTGTAACTATGCACAACACGGCCAGCCTTTTCAGAATCTGCGCAACGTGAAAGGAAAAATTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACt                                                                                   <  1:785280/142‑1 (MQ=255)                                                                   acctttttGCGTCTGATCTTCTCTCAGGTGGACAATGCAAAACACGGACGGCGCATTAAAAATCTGCGCAACGAAAGAAGAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAg                                                                              <  1:378421/144‑1 (MQ=255)                                                                   aaCTTTTTGCGTTTGACCTTCTCTAGTGGTGATTTGGCAAAACCGGGCCAGCGCTTTAAAATTCTGCACAAGGTAAGAAGAAAAACTGAAAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCCCCATGAAACTGGaa                                                                               <  1:672360/150‑1 (MQ=255)                                                                   aaCGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGa                                                                                >  2:216234/1‑149 (MQ=255)                                                                       ttATGCTTCGAAACTTCTCTCAGGGTGACTAGACAGAACACGGTCAGCGCATTAAGAACCGGCGCAAGGTGATGAGAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCg                                                                           <  2:477417/150‑1 (MQ=255)                                                                           gcttctaaccTTCTCTCATGGTGACTATGAAAACCCCGGTCAGCGCTTTAAAAATCTGCGCAACGTGATGAGAAAAACTGATAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTa                                                                        <  2:60234/140‑1 (MQ=255)                                                                            cGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacg                                                                     >  1:301431/1‑151 (MQ=255)                                                                              tCTGACCTTCTCTCATGGTGACTATGCAAAACACGGTCAGCGCATTAAGAACCGGCGCACCGTGATGAGAAAAACTGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCgg                                                                          <  2:541371/144‑1 (MQ=255)                                                                              tCTGACCTTCTCTCATGGTGACAATGCAAAACCCGGCCAGCGCATTCAAAATCTGCGAAAGGTGATGAGAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTa                                                                        <  2:396/146‑1 (MQ=255)                                                                                     ttCTCTCAGGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGAAACGTGAGGAGAAAAACTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGttt                                                               <  2:221422/148‑1 (MQ=255)                                                                                        tctcATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTg                                                          >  2:622811/1‑150 (MQ=255)                                                                                             tGGTGAATAGGAAAAACACGGACAGCGCATCCAGATTCTGCGAAACGTGATGAAAAAAATTGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTctct                                                           <  2:443107/144‑1 (MQ=255)                                                                                              gtgaaCTATGCAGAACCCGGTCAGCACATTAAGAATCTGCCCAACGTGATGAGAAAAAGGGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCt                                                    <  2:370180/146‑1 (MQ=255)                                                                                              ggtaattaggaaaaaCCCGGTCAGCGATTTCAAAATCGGCGAAAGGTGATGAGAAAAACGGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCt                                                    <  2:530508/137‑1 (MQ=255)                                                                                                tGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTgg                                                  >  1:58073/1‑150 (MQ=255)                                                                                                    tATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                                >  2:107359/1‑148 (MQ=255)                                                                                                                    aGCGTATTCAAAATCTGCGAAAGGTGAGGAACAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcacc                               <  1:669786/149‑1 (MQ=255)                                                                                                                    aGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcaccac                             >  1:67007/1‑151 (MQ=255)                                                                                                                         aTTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGAt                         >  1:803020/1‑150 (MQ=255)                                                                                                                            cAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAAt                     >  2:88669/1‑151 (MQ=255)                                                                                                                             aGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATc                    >  1:437165/1‑151 (MQ=255)                                                                                                                             aGAATCCGGGCAAGGTGATGAGAAAAACGGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATa                        <  2:454125/147‑1 (MQ=255)                                                                                                                                accggataaaggagatgaAAAAAACAGAAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATaa                       <  1:675247/132‑1 (MQ=255)                                                                                                                                              atgaGAAAACATGGAAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTAt              <  2:740064/140‑1 (MQ=255)                                                                                                                                                gaGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGa  >  1:109509/1‑150 (MQ=255)                                                                                                                                                 accAAACCTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCg   <  2:149056/146‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                   GTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGTAAAACCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGA  >  NC_000913/1755716‑1756008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑