Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,862	0	C	A	42.4%	52.7 / 12.7	34	S55R (AGC→AGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base C (15/4);  new base A (0/14);  total (15/19)
Fisher's exact test for biased strand distribution p-value = 6.06e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAA  >  NC_000913/1755718‑1756009                                                                                                                                                 |                                                                                                                                                      ttGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCaaaa                                                                                                                                                   <  2:540031/149‑1 (MQ=255)   gCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTg                                                                                                                                                <  2:535710/150‑1 (MQ=255)       cATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑aaa                                                                                                                                          <  1:315049/151‑1 (MQ=255)       cATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑a                                                                                                                                            >  2:643612/1‑149 (MQ=255)                                 agaTGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCa                                                                                                                >  1:344000/1‑150 (MQ=255)                                        agaaaaaaggggggACGCGGGCATAACCGTTGCCCGTCTGACCTTCTCTCAGGGTGAATATGAAAAACGCGGCCAGCACTTCCAGATTCGGCGCAACGTAGAGAGAAAAACTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTc                                                                                                          <  2:702954/137‑1 (MQ=255)                                          cTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCgg                                                                                                       >  1:94024/1‑150 (MQ=255)                                           aaaaaGGCGGGCCGCTGGCATGAACGTTATGCGTCTAACCTTCTCTCATGGTGACTATGCAGACCACGGCCAGCGCATTAAAAATCGGCGCAACGTGAGGAGAAAAACGGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCgg                                                                                                       <  1:353428/148‑1 (MQ=255)                                            aaaaTGCTGGCCGCGGGATGGAACGTTATGCGTCTGAACTCCTCTCATGGTACATAAACAAAACACGTTCAGCGCATTCAGAATCGGCGCAACGAAAGGACAAAACCGGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGaa                                                                                                     <  2:387897/150‑1 (MQ=255)                                            aaaaTGCTGGACGCTGGCAAAAACGTTATGCTTCTTAACTTCTCTCTTGTTGACTATGAAAACCACGGTCAGCGCATTCAGAATCTGCACAATGTTATGAGAAAAACTGTA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGaa                                                                                                     <  1:732694/150‑1 (MQ=255)                                                    ggACGTGGGCATGAACTTTTGGCGTCTAATCTCCTCTAAGGGTGACAAGACAAAAACCGGGAAGCCAATTAAAAATCGCCGCACGGTGATAAGAAAAAGTGAA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAcc                                                                                            <  2:359503/151‑1 (MQ=255)                                                     gACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCAcc                                                                                            >  2:15367/1‑150 (MQ=255)                                                        gCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATg                                                                                         >  1:272117/1‑150 (MQ=255)                                                                 aaCGTTATGCGTCTGACCTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGAGGAGAAAAACTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAg                                                                               <  1:759697/151‑1 (MQ=255)                                                                         gCGTCTGAACTTCTCTCATGGTGACTATGCAGAACCCGGTCAGCGCATTAAGAATCTGCCCACCGTGATGAGAAAACCTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCgg                                                                           <  1:94814/147‑1 (MQ=255)                                                                                         cATGGTGATTATGAAAAACGCGGTCAGCGCATTCAGAATCGGCGCAAGGTGATGAGAAAAACTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGa                                                          <  1:836812/148‑1 (MQ=255)                                                                                           tGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCt                                                     >  1:361228/1‑151 (MQ=255)                                                                                              taaCTATGAAAACCACGTTCAGCGCATTCAAAATCTGCGCAACGTGATGAAAAAAACTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTgg                                                   <  1:250972/148‑1 (MQ=255)                                                                                              tGACTATGAAAAACCCGTTCAGCCTTTTCAAAATCTGCGAACTGTGAGGAAAAAATCTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTctct                                                            <  1:95570/141‑1 (MQ=255)                                                                                                aCTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                                 >  1:18455/1‑150 (MQ=255)                                                                                                   aggCAGAACACGGTCGGCGCTTTCAGAATCTGCGCAACGTGATGAG‑AAAAATGGTAAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGa                                              <  1:742855/148‑1 (MQ=255)                                                                                                       acacccctgtaaGCGCATACAGACTCGCCGCAGAGTAAAAAGCAAAATTAGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAAGCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCtt                                          <  2:17950/139‑1 (MQ=255)                                                                                                       aGAACCCGGACAGCGCATTAAGAATCTGCGCAACGTAAGGAGAAAAATTGAA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGAc                                             <  2:54422/147‑1 (MQ=255)                                                                                                           cacGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACtt                                     >  2:782573/1‑151 (MQ=255)                                                                                                            acGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACttt                                    >  2:100310/1‑151 (MQ=255)                                                                                                              ggTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTc                                   >  2:80991/1‑150 (MQ=255)                                                                                                                        ttaaaaaTCTGCGCAACGTGATGAAAAAAACTGGA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcacca                               <  1:729265/139‑1 (MQ=255)                                                                                                                            gAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCt                    >  1:156133/1‑151 (MQ=255)                                                                                                                            gAATCAGCGCAAGGTGAT‑AAAAAAACCGGA‑AAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACttt                                    <  2:482636/135‑1 (MQ=255)                                                                                                                                  gcgcAACGTGATGAGCAAAACTGGT‑AACA‑CCGCCGCTATCCGGCTTGATACGAAAGGGCCGGAAATCCGCACCATGCAACTGGAAAGCGTTAAAGACGTTTCTCTGAAACCTGGACAGACCTTTACTTTCACCACTGATAAATCTGTTATc              >  2:555557/1‑151 (MQ=255)                                                                                                                                      aaCGTGATGAGAAAAACTGAA‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGc           <  1:15369/150‑1 (MQ=255)                                                                                                                                         gTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAAc        >  2:301689/1‑150 (MQ=255)                                                                                                                                          tgatgaGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAAc        >  2:29497/1‑149 (MQ=255)                                                                                                                                               aGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGaa  >  1:819216/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                      TTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAACTTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGGT‑AAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGCAACAGCGAA  >  NC_000913/1755718‑1756009

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑