Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,578,143	0	A	C	43.8%	65.6 / 20.7	48	L79V (TTA→GTA)	maeB	malic enzyme: putative oxidoreductase/phosphotransacetylase
Reads supporting (aligned to +/- strand):  ref base A (25/2);  new base C (0/21);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.13e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGTTCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGCC  >  NC_000913/2577994‑2578291                                                                                                                                                            |                                                                                                                                                     tggttCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑Ac                                                                                                                                                     >  2:377797/1‑151 (MQ=255)  ggttCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑Acc                                                                                                                                                    >  1:553669/1‑151 (MQ=255)          cgcgGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCAcc                                                                                                                                            >  1:415020/1‑151 (MQ=255)                            aattttGCCCGGGTAGAGTCCGTCACCTT‑AATGTTAAATTACATCACCCCGGGCGAATTTCTAAAACAGACCGCCCTT‑CCCTCCCACCCCGGGTTTG‑CC‑TGCAAGCGCGCAAATGTT‑GCCAA‑CCCCCACCACCGCCGTACCGTTAGAGAt                                                                                                                           <  2:130493/147‑1 (MQ=255)                            aaaTTTGTCCGGGTCGAGTTAGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTag                                                                                                                               >  2:496339/1‑146 (MQ=255)                                   tCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGcc                                                                                                                    >  1:619323/1‑150 (MQ=255)                                      gggTCGATTTCGTCACCTTCAATGTCAAA‑TACACCAACCCCGGCGATTTTCTTAAACAGACCGCCCTT‑GCCTTCCATCCCCGGTTTG‑CC‑TGCCAGCGCCCCAATTTT‑GCCTA‑CCCCCAGCCCCGCCGTACCGTTAGAGATCACCGcc                                                                                                                    <  1:132041/147‑1 (MQ=255)                                      gggTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGccacc                                                                                                                 >  2:387266/1‑150 (MQ=255)                                              ttCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCt                                                                                                        >  1:745647/1‑151 (MQ=255)                                                     aCTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCgg                                                                                                 >  1:36444/1‑151 (MQ=255)                                                     aCTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCAGGCgg                                                                                                 >  1:471745/1‑151 (MQ=255)                                                      cTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGt                                                                                                >  1:660306/1‑151 (MQ=255)                                                       ttaaatataaaa‑TACACCAACCCCGGCAATTTTCTTAAAACGACCCCCTTT‑CCCTTCCTCCCCGGGTTTC‑CT‑TGCCAGCCCGCAATTGTG‑CCCTA‑ACCCCCGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCg                                                                                                      <  2:608486/135‑1 (MQ=255)                                                       ttaaaTGTAAAA‑TACATCAACCCCGGCGATTTTCTAAAACAAACCGCCTTT‑CCCTCCCATCCCCGTTTTG‑CC‑GGCCAGCGCGCAAATGTT‑GCCAA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGt                                                                                                <  1:508859/147‑1 (MQ=255)                                                       ttCGATGTCAAA‑TACATCAACCCCGGCAAATTTCTAAAACAGAACGCCCTT‑CCCTCCCATCACCGGTTTG‑CC‑TGCCAGCGCGCAAATGTT‑CCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCgg                                                                                                     <  1:3201/145‑1 (MQ=255)                                                                aaa‑taaatCAACCCCGGCGATTTTCTAAAACAGACCCCCCTT‑CCCTCCCACCCCCGTTTTG‑CC‑TGCCAGCGCCCCAATGTT‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTa                                                                                       <  2:296790/150‑1 (MQ=255)                                                                aaa‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGt                                                                                        >  2:386558/1‑149 (MQ=255)                                                                aaa‑TACACCAACCCCGGCAAATTTCTAAAACAGACCGCCCTT‑GCCTCCCATCCCCGGTTTG‑CC‑GGCCAGCGCGCAAATGTT‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTa                                                                                       <  1:139729/150‑1 (MQ=255)                                                                aaa‑TACAACAACCCCGGCGAA‑TTCTTAAAAAAAACCCCCTTCGCCTCCCATCCCCGGTTTC‑CC‑TGCCGGCGCGCAAATGTT‑CCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAg                                                                                      <  1:710460/151‑1 (MQ=255)                                                                aaa‑TACAAAAATCCCGGAGATTTTCTAAAAAAAACCCCCTTT‑CCCTCCCACCACCGGTTTC‑CC‑GCCCGCCCCCCCATTGTG‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTg                                                                                         <  2:708660/148‑1 (MQ=255)                                                                     aCATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtt                                                                                  >  2:351350/1‑151 (MQ=255)                                                                       aTCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtttt                                                                                >  1:732528/1‑151 (MQ=255)                                                                          aaccccGGCAATTTTCTAAAACAG‑ACCCCCTT‑TCCCTCCCACCCCGGTTTGCCC‑GGCCGGCGCCCCATTGTG‑GCCTA‑CCCCCGGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtttt                                                                                <  2:630826/145‑1 (MQ=255)                                                                          aaTCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAAc                                                                             >  1:429688/1‑151 (MQ=255)                                                                             cccGGCGAATTTCTTGAACAGAACCCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAACGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTAAGAGATCCCCGCCACCAGGGTCCCTCGGGCGGCATATTTGTAGGCTTTCACCggg                                                                          >  2:688625/1‑151 (MQ=255)                                                                             cccGGCGAATTTCAAAAACAAACCCCCTTT‑CCCTTCCA‑CCCCCGTTTG‑CCGTGCCGGCGC‑CCCATGTTCGCCAA‑CCCCCGGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACgg                                                                           <  2:185958/150‑1 (MQ=255)                                                                              ccGGGGAATTTTTAAAACACGACCCCCCT‑CCCCTCCCCCCCCGGGTTGCCC‑TGCCCGCGCGCAACGGTG‑CCCAA‑ACCCCCGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCtt                                                                                  <  1:444617/143‑1 (MQ=255)                                                                                ggCAAATTCCTAAAAAAAACCCCCCTT‑GCCTCCCTCCCCCGGTTGC‑CC‑TGCCAGCGCCCCAATTTT‑CCCTA‑CCCCAACCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGt                                                                         <  1:492326/149‑1 (MQ=255)                                                                                    aaTTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCttttt                                                                   >  2:475097/1‑151 (MQ=255)                                                                                       ttCTTAAACAGACCCCCCTT‑GCCCCCCACCCCCGTTTGG‑CC‑GCCCACGCCGCCAATTTC‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCTCCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCttttt                                                                   <  2:84701/148‑1 (MQ=255)                                                                                          taaaccagcccccccTT‑GCTTCCCACCCCCGTTTTG‑CC‑AACCACCCCCCCAATGTT‑CCTTA‑CCCCAAGAACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCttttt                                                                   <  1:115693/133‑1 (MQ=255)                                                                                           tAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTc                                                            >  2:454944/1‑151 (MQ=255)                                                                                            aaaaAGACCGCCTTA‑CCCTTCCATCCCCGTTTGC‑CC‑TGCCGGCGCCCAAATTTG‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                                           <  1:670783/151‑1 (MQ=255)                                                                                            aaaaAGACCGCCC‑T‑GCCCTCCTACCCCGTTTTG‑GC‑CTCCAGCGCCCCAAAGGT‑GGCAACCCCCCGGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCtttg                                                                    <  2:538772/142‑2 (MQ=255)                                                                                            aaaCAGACCCCCCTT‑CCCTCCCACCCCGGGTTTC‑CC‑GGCCGGCGCCCCATTTTT‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGAttt                                                             <  1:136549/149‑1 (MQ=255)                                                                                            aaaCAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTc                                                            >  2:681157/1‑150 (MQ=255)                                                                                              aCAGACCCCCCTT‑CCCTCCCACCCCCGGTTTG‑CC‑GGCCGGCGCGCAATTGTT‑GCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAg                                                         <  1:139089/151‑1 (MQ=255)                                                                                               cAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCa                                                           >  1:677548/1‑148 (MQ=255)                                                                                                  accccccTT‑CCCTCCCATCCCGGTTTTG‑CC‑TGCCGGCGCCCAAATGTT‑CCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGa                                                        <  1:598576/144‑1 (MQ=255)                                                                                                      cccTT‑GCCTCCCACCCCCGTTTTG‑CC‑TGCCAGCGCCCAAATTTT‑CCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGt                                                  <  1:311989/150‑1 (MQ=255)                                                                                                              cTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATCTTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCACGACAAGGTGCGGCAAc                                          >  1:204825/1‑151 (MQ=255)                                                                                                                    tCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTgg                                    >  2:113409/1‑151 (MQ=255)                                                                                                                     cACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTgg                                    >  2:737931/1‑150 (MQ=255)                                                                                                                            ttG‑CC‑TGCCAGCGCGCAATTGTT‑CCCTA‑CCCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAg                             <  1:521904/150‑1 (MQ=255)                                                                                                                              g‑cc‑tgccAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGcc                          >  2:67729/1‑151 (MQ=255)                                                                                                                                             ccAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATcgc             >  1:218601/1‑151 (MQ=255)                                                                                                                                                    tgcccTA‑CCCCCAGCCCCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCa                   <  2:677511/136‑1 (MQ=255)                                                                                                                                                         tA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGcc  >  1:63883/1‑151 (MQ=255)                                                                                                                                                            |                                                                                                                                                     TGGTTCGAGCGCGGCGACAACTTCAATAAATTTGTCCGGGTCGAGTTCGTCAACTTCAATGTCAAA‑TACATCAATCCCGGCGAATTTCTTAAACAGAACGCCCTT‑GCCTTCCATCACCGGTTTG‑CC‑TGCCAGCGCGCCAATGTT‑GCCTA‑ACCCCAGCACCGCCGTACCGTTAGAGATCACCGCCACCAGGTTACCTCGGGCGGTATATTTGTAGGCTTTTAACGGGTCTTTTTCGATTTCAAGACAAGGTGCGGCAACGCCTGGTGAGTAGGCCAGCGCCAGATCGCGCTGTGTTGCC  >  NC_000913/2577994‑2578291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑