Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,431	0	A	C	40.4%	60.6 / 16.6	52	G34G (GGT→GGG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (18/13);  new base C (0/21);  total (18/34)
Fisher's exact test for biased strand distribution p-value = 5.06e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGA  >  NC_000913/2248288‑2248577                                                                                                                                                 |                                                                                                                                                    aaCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTAc                                                                                                                                              <  2:224389/151‑1 (MQ=255)  aCGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTAcc                                                                                                                                             <  1:392822/151‑1 (MQ=255)     aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGAt                                                                                                                                          >  2:708524/1‑151 (MQ=255)     aaCCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGAt                                                                                                                                          <  1:81392/151‑1 (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)                                                                                                                                   ggggaaaaaaaaaGCCCTGCCCCAATGAAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATg                    <  1:223058/135‑1 (MQ=255)                                                                                                                                    agaaaaaaaaaaGCCTTGTCCCGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcg               <  1:364360/140‑1 (MQ=255)                                                                                                                                    agGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGAt           >  1:531938/1‑151 (MQ=255)                                                                                                                                       caacaaAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCAGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGt        >  1:500548/1‑151 (MQ=255)                                                                                                                                         aaaaaagGACCTGTACCGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGAtt          <  2:605226/145‑1 (MQ=255)                                                                                                                                             aaaGACCTTACCCGAGGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGa  <  2:728712/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    AACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGG‑ACCTGCCTGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAA‑CCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAGA  >  NC_000913/2248288‑2248577

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑