Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,755,862	0	C	A	42.1%	50.2 / 19.0	38	S55R (AGC→AGA)	pykF	pyruvate kinase I
Reads supporting (aligned to +/- strand):  ref base C (16/6);  new base A (0/16);  total (16/22)
Fisher's exact test for biased strand distribution p-value = 4.62e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGC  >  NC_000913/1755713‑1756000                                                                                                                                                       |                                                                                                                                             aTTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGc                                                                                                                                              >  2:46403/1‑150 (MQ=255) aTTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGc                                                                                                                                              >  1:562180/1‑150 (MQ=255)   tGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCaa                                                                                                                                            >  1:704653/1‑150 (MQ=255)    gTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCaaa                                                                                                                                           <  2:118502/150‑1 (MQ=255)       tGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACt                                                                                                                                        <  2:230414/150‑1 (MQ=255)                 gcccGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTTGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCGACGTGATGAGCAAAACTGG‑TAAAA‑ccgc                                                                                                                           >  2:440166/3‑151 (MQ=255)                       aaaCCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTAt                                                                                                                     >  1:15754/1‑151 (MQ=255)                           cGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTg                                                                                                                 >  2:479857/1‑151 (MQ=255)                               tCTGAAGCGACGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTg                                                                                                             >  2:88170/1‑151 (MQ=255)                                         ttttAGCAAAAATGCTGGACGCTGGAAGAAACGTTATGCTTCAAAAC‑TTCTCTCATGGTGACTATGAAGAACACGGTCGGCCCATTCAAAATCTCCGAACCGTGATGAGAAAAACTGG‑AAAAA‑CCGCCGCTATCCTGCTTGATACCa                                                                                                       <  1:644182/145‑1 (MQ=255)                                         ttttAGCAAAAATGCGGGCCGCGGGAAGGAATTTTATGCTTCTGACC‑TTCTCTCATGGTGATTATGCAAACCACGGTCAGCGAATTCAGAATCGCCGAAAGGTGATGAAAAAAACTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCaa                                                                                                      <  2:399360/146‑1 (MQ=255)                                                 aaatTGCTGGACGCGGGAATGACCTTTATGCTTCTGACC‑TTCTCTCATGGTGACTAGGCAAAACACGGCCGGCTCATTCAAATTCGGCGCAAGTTGAGGAGAAAACTTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGa                                                                                             <  1:100296/149‑1 (MQ=255)                                                  aaaTGCTGGACGCTGGAATGAACTTTATGCTTCTAACC‑TTCTCTGATGTTGACTATAAAAAACACGGTCCGCGCATTCAGAATCTGCAAAGGGTAATAAAAAAAAGTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAAt                                                                                          <  2:686016/151‑1 (MQ=255)                                                   aaTGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATc                                                                                         >  2:701774/1‑151 (MQ=255)                                                       cTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGc                                                                                      >  2:586732/1‑150 (MQ=255)                                                        tggccgtgggaaTGAACGTTTTGCTTCTAACC‑TTCTCTCAGGGTGACTATGCAGACCACGGCCAGCGCATCAAGAATCCGCGAACGGGGATGAGAAAACCTGG‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCa                                                                                     <  1:536439/139‑1 (MQ=255)                                                         ggACGCGGGAATAAACTTTATGCTTCTGACT‑TTCTCTCAGGGTAACTATGAAAACCCGGGACAGCGCTTGAAGAATCTGCGAAACTTGAGGAAAAAAAGGGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATcc                                                                                        <  2:520123/146‑1 (MQ=255)                                                           aCGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCAt                                                                                 >  1:443210/1‑151 (MQ=255)                                                                ggcaaaaccgtattGCGTCTAACC‑TTCCCGCGGGGTGATAAGGCAAAACCCGGTCAGCCCATCAAAAATCTGCGCAAGGTAAT‑AACAAAACCGGAAAAAA‑CCGCCGCTATCCCGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAAc                                                                            <  2:699634/138‑1 (MQ=255)                                                                ggaaTGAACTTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGAAAAACACGGCCAGCGCATTAAGAATCGGCGAAAGGTGAGGAGAAAAACTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAAc                                                                            <  1:152500/148‑1 (MQ=255)                                                                ggCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCG‑CGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGaaa                                                                             <  1:597565/149‑1 (MQ=255)                                                                      atcGTTATGC‑TTTGAACTTTCTCGCAGGGGGATTATGAAAAACACGGCCAGCGCATACAAATTCCGCGCACGGTAATAAACAAAAGTGA‑AAAAC‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTg                                                                          <  2:542096/145‑1 (MQ=255)                                                                      aaCGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGa                                                                        >  2:602402/1‑149 (MQ=255)                                                                         gTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCg                                                                   >  1:278818/1‑151 (MQ=255)                                                                                 tCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAacgac                                                           >  1:476208/1‑151 (MQ=255)                                                                                         ttCTTTCAGGGTGATTATGCAGACCAGGGGCAGCGCATACAGAATCTGCGCACCTTGAGGAGAAAAACTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTa                                                                <  1:252780/139‑1 (MQ=255)                                                                                              tcAGGGTGAGTATGCAAAACACCGCCAGCCCATTCACAATGCGCGCAAGGGGACGACAAAAACTGG‑CAAAA‑CCGCCGCTATCCTGCTTGATGCCAAAGGTCCGGAAGGCCGCACCATGAAACTGGAAGGCGGTAACGACGtt                                                        <  2:528292/142‑1 (MQ=255)                                                                                                  ggtaataaggCAGAACCCGGCCAGCGCTTTCAGAATCCGCGCAACGTGAGGAAAAAACCTGG‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTg                                           <  2:64384/142‑1 (MQ=255)                                                                                                    tGATTACGCAGAACGCGGGCAAGGAATTCAAATCCTGCTAACCGGGATAAGCAAAA‑TGG‑AAAAACCCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTgg                                          <  1:471490/150‑1 (MQ=255)                                                                                                      actacacAGAACGGGGTCAGCGCATACAGAACCTGCCAAACGTAAAGAGAAAAACGGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGt                                         <  2:57747/143‑1 (MQ=255)                                                                                                       cTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTc                                        >  2:513682/1‑149 (MQ=255)                                                                                                              gAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCttt                                >  2:389568/1‑150 (MQ=255)                                                                                                                 cacGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACtt                            >  1:424595/1‑151 (MQ=255)                                                                                                                     gTCAGCGCTTACAGAATCTGCACAGTGTGGTGAAAAAAACGGT‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTca                         <  1:238013/150‑1 (MQ=255)                                                                                                                       cAGCGCATTCAAAATCTGCGCAAGGTGAGAAAAAAAACGGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTcacca                      <  2:278792/151‑1 (MQ=255)                                                                                                                          cgcATTCAAATTTTGCGAAAGGTGATAAAAAAAACTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACt                    <  2:528527/150‑1 (MQ=255)                                                                                                                                 aaaaTCTGCGCAACGTGATAAAAAAAACTGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATaaa              <  2:24554/147‑1 (MQ=255)                                                                                                                                 aGAATCTGCGCAAGGTGAGGAAAAAAACGGA‑AAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATaa               <  2:704442/148‑1 (MQ=255)                                                                                                                                       tGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTAt      >  2:57918/1‑151 (MQ=255)                                                                                                                                            aaCGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGc  >  2:323565/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                             ATTGTTTGCACCATCGGACCGAAAACCGAATCTGAAGAGATGTTAGCTAAAATGCTGGACGCTGGCATGAACGTTATGCGTCTGAAC‑TTCTCTCATGGTGACTATGCAGAACACGGTCAGCGCATTCAGAATCTGCGCAACGTGATGAGCAAAACTGG‑TAAAA‑CCGCCGCTATCCTGCTTGATACCAAAGGTCCGGAAATCCGCACCATGAAACTGGAAGGCGGTAACGACGTTTCTCTGAAAGCTGGTCAGACCTTTACTTTCACCACTGATAAATCTGTTATCGGC  >  NC_000913/1755713‑1756000

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑