Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,424	0	C	A	41.7%	67.0 / 26.6	48	V37F (GTT→TTT)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base C (19/9);  new base A (0/20);  total (19/29)
Fisher's exact test for biased strand distribution p-value = 6.36e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGT  >  NC_000913/2248279‑2248571                                                                                                                                                   |                                                                                                                                                     tAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACaaaa                                                                                                                                                  >  1:302421/1‑150 (MQ=255) tAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCAAGTTCACAGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACaaa                                                                                                                                                   >  2:457153/1‑149 (MQ=255)          aaCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTAc                                                                                                                                        <  2:224389/151‑1 (MQ=255)           aCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTAcc                                                                                                                                       <  1:392822/151‑1 (MQ=255)              aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGAt                                                                                                                                    <  1:81392/151‑1 (MQ=255)              aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGAt                                                                                                                                    >  2:708524/1‑151 (MQ=255)                  ggAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGa                                                                                                                                 >  2:461767/1‑150 (MQ=255)                     aaCCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑cct                                                                                                                            <  2:174869/151‑2 (MQ=255)                         ggCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCaa                                                                                                                        <  1:410318/151‑1 (MQ=255)                              atagGCGGCCAGTCAACCGAGCCGGGTCATCAGAAAGTAAACCAACAGGCCAATAAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCGGAGAAATCGTTGCGCCGGAGGCAAAAAAAAGACCTGTCCCGATGGAA‑CCGCCAATGGc                                                                                                                    <  2:274212/150‑1 (MQ=255)                                    aGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAatcat                                                                                                              >  1:573053/1‑150 (MQ=255)                                      ccattcccccGAGACGGATCATCAGAAAAAAAACCACCAGCCCAACCAGCATATCCGAGACCAACCCCCCCCCCGC‑CCCCGCCTGAAAAATCGTTGCGCCAGAGGCAAAAAAAAGCCCTGTCCCAATGAAA‑CCGCCAATGGCAatc                                                                                                                <  2:701165/138‑1 (MQ=255)                                                  gaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACgcgc                                                                                               >  1:118908/1‑151 (MQ=255)                                                   aCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGcc                                                                                              >  2:117574/1‑151 (MQ=255)                                                      ggTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCttt                                                                                           >  1:184452/1‑151 (MQ=255)                                                      ggTAATAAGGAAGAAAACCACCGGGCAAACCAGCATAGAGGAAAACAAGGCCCCCCCCGG‑ACCTGCCGGAAAAATGGTGGCGCCGGAGGAAAAAAAAAGCCCTGTCCGGGTGGAA‑CCGCCAATGGCAATCATCGTCAgg                                                                                                       <  2:132833/139‑1 (MQ=255)                                                              gaaaaaaacccATCGGCCCAATCAGAATATAGGAG‑GCAATCCCCCCCCCGGCCCCTCCCGGAAAACTCTTTGCGCGAGAGGCAAAAAAAACCCCTGCCCCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCAc                                                                                    <  2:246505/141‑1 (MQ=255)                                                                aaaaaaaCCATCAGGCCAATCAGCATATACGAGAGCAACCCCCCGCCCGG‑ACCTGCCTGAAAAATCGTTGCGCCAGAGGAAAAAAAAAGCCCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACg                                                                                   <  1:691531/145‑1 (MQ=255)                                                                               ccAAACAGCATAAACGAGACCAACCCCCCGCCCGG‑CCCTGCCTGAGAAATCGTTGCGCCAGAGGCAAAAAAAAGACCTGTCCCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCt                                                                   <  2:781222/150‑1 (MQ=255)                                                                                cAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                                  >  1:27221/1‑150 (MQ=255)                                                                                 aaccagaataaccGAGAGCAATCCCCCCCCCGG‑CCCTGCTTGAAAAATCGTTCCGCCAGAGGAAAAAAAAAGCCCTGTCCCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                                  <  1:780167/137‑1 (MQ=255)                                                                                     aGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTgg                                                            >  2:336932/1‑151 (MQ=255)                                                                                       caaaaaCGAGACCAAGCCCCCTCCCGG‑CCCTGCCTGAAAATTCGTTGCGCCAGAGGCAAAAAAAAGCCCTTTCCCGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGt                                                           <  2:570270/145‑1 (MQ=255)                                                                                        aaaaaCGAGAGCAACCCCCCCCCCGG‑CCCGGCCGGAGAAACCGTGGCGCCAGAGGCAAAAAAAAGCCCTGACCGGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtt                                                          <  2:476414/146‑1 (MQ=255)                                                                                          ataGGAGAGCAATCCCCCGCCCGG‑CCCTGCCTGAAAAATCGTTGCGCAAGAGGAAAAAAAAAGCCCTGTCCCGAGGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtttt                                                        <  1:605682/150‑1 (MQ=255)                                                                                                gagCACTCCCCCCCCCGG‑CCCGGCCTGAAAAATCTTCGCGCAAGAGGCAAAAAAAACCCTTGTCCCGTTGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTc                                                  <  1:467172/150‑1 (MQ=255)                                                                                                gagCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCg                                                 >  2:726335/1‑151 (MQ=255)                                                                                                 accacccccccccccGC‑CCCTGCCGGAAAAGCCGTGGCGCAAGAGGAAAAAAAAACCCCGCCCCCGAGGAAC‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGtttt                                                        <  2:302471/136‑1 (MQ=255)                                                                                                        ccccGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCAt                                         >  2:409882/1‑151 (MQ=255)                                                                                                         cccccccgG‑CCCTGCCTGAAAAATCGTGGCGCCAGAGGAAAAAAAAAGCCCTGTCCCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATa                                        <  1:372235/151‑1 (MQ=255)                                                                                                                gg‑ACCTGCATGAGAAATCGTGGCGCCAGAGGCAACAAAAAGACCGGTATCGATGGAA‑CCGCCAATGGCAATCATCGTATGGTGACGCGACTTTAATTCACGGCAGAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                 >  2:305440/1‑151 (MQ=255)                                                                                                                 gaccctgcctgAGAAATCGTGGCGCCAGAGGAAAAAAAAAGCCCTGTCCCGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                 <  2:42856/148‑1 (MQ=255)                                                                                                                  accctgccggAGAAATCGTTGCGCCGGAGGAAACAAAAAGACC‑GGGCCGAAGGAACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaaaa                                  <  2:706936/147‑1 (MQ=255)                                                                                                                   cccggcgggaaaaaCCGTGGCGCCAGAGGCAACAAAAAGCCCTGTACCAATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                 <  2:258843/138‑1 (MQ=255)                                                                                                                        cgtgAAAAATCTTTGGCCAAGAGGAAAAAAAAATACTTTTACGGAGTAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTAt                            <  1:536896/147‑1 (MQ=255)                                                                                                                        cctgAAAAATCGTTGCGCCAGAGCAAACAAAAAGACCTGTCCCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATcc                          <  1:383296/151‑1 (MQ=255)                                                                                                                         ggaaaaatgcGTTGCGCCAGAGGAAAAAAAAAAACCTGTCCGGATGGAC‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTa                             <  2:727930/138‑1 (MQ=255)                                                                                                                          tgAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCAt                        >  1:151150/1‑151 (MQ=255)                                                                                                                          tgAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCAt                        >  1:749587/1‑151 (MQ=255)                                                                                                                            agaAACCGTGGCGCCAGAGACAACAAAAAGCCCTCTCCGGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATc                       <  2:648253/150‑1 (MQ=255)                                                                                                                             gaAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                     >  2:216437/1‑151 (MQ=255)                                                                                                                              aatgcGTTGCGCCAGAGGCAAAAAAAAGCCCTGCACCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTa                    <  1:157330/147‑1 (MQ=255)                                                                                                                              aaaTCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                     >  2:760120/1‑150 (MQ=255)                                                                                                                                aTCGTTGCGCCAGAGCCAAAAAAAAGCCCTTTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaa                  <  1:601634/151‑1 (MQ=255)                                                                                                                                       cgcCAGAGGAAAAAAAAAGCCCTGTCCCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaaa                 <  1:760220/145‑1 (MQ=255)                                                                                                                                          cAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcgc        >  1:755909/1‑151 (MQ=255)                                                                                                                                           agagcaaacaaAAAGCCTTTTACGGGTGGAA‑CCGCCAATGGCAATCATCGTCAGATGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcgc        <  2:419705/144‑1 (MQ=255)                                                                                                                                           agagCCAAAAAAAAGCCTTGACCCGATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAg            <  2:221984/146‑1 (MQ=255)                                                                                                                                             agGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGAt     >  1:531938/1‑151 (MQ=255)                                                                                                                                                caacaaAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCAGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt  >  1:500548/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                     TAAGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGT  >  NC_000913/2248279‑2248571

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: ‑