Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,248,431	0	A	C	41.3%	81.8 / 14.2	46	G34G (GGT→GGG)	lysP	lysine transporter
Reads supporting (aligned to +/- strand):  ref base A (24/3);  new base C (0/19);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 3.71e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAG  >  NC_000913/2248281‑2248576                                                                                                                                                         |                                                                                                                                                  aGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGa                                                                                                                                                   <  1:31992/151‑1 (MQ=255)                ggAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGaa                                                                                                                                    <  1:606047/151‑1 (MQ=255)                 gAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAAc                                                                                                                                   >  1:244130/1‑151 (MQ=255)                  aaaCCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAAcc                                                                                                                                  >  2:19004/1‑151 (MQ=255)                                       aatCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGAGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTc                                                                                                               >  1:282079/3‑149 (MQ=255)                                         tCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGt                                                                                                           >  2:477692/1‑151 (MQ=255)                                          cACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTg                                                                                                          >  1:648514/1‑151 (MQ=255)                                             cGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcg                                                                                                       >  2:485073/1‑151 (MQ=255)                                              gagaCTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGAcgc                                                                                                      >  2:139983/1‑151 (MQ=255)                                               agacgggtaacaaGGAAGAAAACCACCAGCCCAATCAGAATAAAGGAGAGCAATCCCCCCCCCGGACCT‑GCC‑GGAAAAATCGTTGCGCAAGAGGCAAAAAAAAGACCTGTACCGAGGAAACCGCCAATGGCAATCATCGTCAgg                                                                                                            <  2:627105/132‑1 (MQ=255)                                               agaCTGGTCATCAGGAAGAAAACCATCAGCCAAATCAGCATATACGAGAGAAATCCCCCCCCCGGCCCT‑GCC‑TGAGAAATCTTTGCCCCAGAGGCAAAAAAAAGCCCTGTACCGATGGATCCGCCAATGGCAATCATCGTCAGGTGa                                                                                                         <  2:663413/147‑1 (MQ=255)                                                  cTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                  >  2:360249/1‑151 (MQ=255)                                                    ggTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCttt                                                                                                >  2:662796/1‑151 (MQ=255)                                                    ggTCAAAAGAAAGAAACCCACCAGCCCAATCAGCATATACGAGAGCAAGCCCCCGCCCGGCCCT‑GCC‑GGAAAAATCGTGGCGCAAGAGGAAAAAAAAAGCCCGGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                  <  1:350368/149‑1 (MQ=255)                                                     gTCAACAGAAAAAAACCCACCAGCCCAAAAAGAATAAACGAGAAAAACCCCCCGCCCGGCCCT‑CCC‑AAAGAATTCGTTGCGCAAGAGGAAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCt                                                                                                  <  1:319889/148‑1 (MQ=255)                                                        atcaGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAAtt                                                                                            >  1:548957/1‑151 (MQ=255)                                                          caGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTc                                                                                           >  1:372073/1‑150 (MQ=255)                                                            ggAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACg                                                                                        >  1:436842/1‑151 (MQ=255)                                                               agaaaccaaccAGGCCAACCAGCATATACGAGAGCAACGCCCCGCCCGGCCCT‑GCC‑TGAAAAATCGTTGCGCCAGAGGAAACAAAAAGCCCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCg                                                                                     <  2:333637/141‑1 (MQ=255)                                                                aaaacccaccaGCCCAACCACCATAAACGAGAGCAACCCCCCGCCCGGACCG‑GCC‑GGAGAAATCGTGGCGCCAGAGGAAAAAAAAACCCCTTTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGt                                                                                    <  1:68063/146‑1 (MQ=255)                                                                   aaCCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTa                                                                                   >  2:546357/1‑149 (MQ=255)                                                                           ggCAAATCAGCATATACGAGAGCAATCCCCCCCCCGGACCT‑GCC‑GGAAAAATCGTGGCGCCAGAGGAAAAAAAAAGCCCTGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCgg                                                                            <  2:224669/148‑1 (MQ=255)                                                                             ccAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                                       >  2:598552/1‑151 (MQ=255)                                                                               aaccAGCATATACGAGAGAAACCCCCCCCCCGGCCCT‑GCC‑TGAAAAATCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCtt                                                                       <  2:436893/146‑1 (MQ=255)                                                                               aaccAGCATACACGAGAGCAACCCCCCCCCCGGCCCT‑GCC‑GGAGAAATCGTTGCGCCAGAGGAAAAAAAAAGCCCTGTACCGAGGGACCCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCt                                                                        <  1:256300/145‑1 (MQ=255)                                                                                   aGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTgg                                                                 >  2:58500/1‑151 (MQ=255)                                                                                         taCGAGAGCAACCCCCCGCCCGGACCT‑GCC‑TAAAAAATCGTTGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGt                                                                <  2:169447/146‑1 (MQ=255)                                                                                            gagaGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGttt                                                        >  2:301431/1‑151 (MQ=255)                                                                                             agagCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTc                                                       >  2:291185/1‑151 (MQ=255)                                                                                             aaagCAACCCCCCGCCC‑GACCC‑GCCGTGAAAAATCGTGGCGCAAAAGGCAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGttt                                                              <  2:387053/142‑1 (MQ=255)                                                                                              agagaaccccccccccGGCCCCGGCC‑AGAAAAACCGTGGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGt                                                          <  1:670121/140‑1 (MQ=255)                                                                                                  acccccccccccGGCCCG‑GCC‑TGAAAAAGCGTGGCGCCAGAGGAAAAAAAAAGCCCTGTCCGGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGa                                                    <  1:291152/145‑1 (MQ=255)                                                                                                      ccccGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCAt                                              >  1:167559/1‑151 (MQ=255)                                                                                                         cgcccgGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATAc                                            >  2:24963/1‑150 (MQ=255)                                                                                                             cgGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACaaaa                                        >  2:59268/1‑150 (MQ=255)                                                                                                              ggccct‑gcc‑tgAAAAATCGTTGCGCCAGAGAAAAAAAAAAGCCCTGCCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                      <  1:128491/148‑1 (MQ=255)                                                                                                              ggACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAAt                                      >  2:547502/1‑151 (MQ=255)                                                                                                                      cc‑tgAAAAATCGTTGCGCCAGAGGCAAAAAAAAGCCCTGTCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTa                                  <  2:212482/148‑1 (MQ=255)                                                                                                                          gagaAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATc                            >  2:740350/1‑151 (MQ=255)                                                                                                                             aagtCGTTGCGCCAAGGGCAAAAAAAAGACCTGCCCCGATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCt                           <  1:598495/146‑1 (MQ=255)                                                                                                                             aaaTCGTGGCGCAAGAGGAAAAAAAAAGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCtt                          <  2:564707/150‑1 (MQ=255)                                                                                                                                      cgcAAGAGCCAAAAAAAAGCCCTGTCCCGAGGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTaaaa                      <  1:604877/145‑1 (MQ=255)                                                                                                                                                aaaaaaaaGCCCTGTCCCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGgcg              <  1:89358/140‑1 (MQ=255)                                                                                                                                                aaaaaaaaGCCCTGCACGTATGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTa      <  1:248454/148‑1 (MQ=255)                                                                                                                                                  caaAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGc    >  2:542864/1‑151 (MQ=255)                                                                                                                                                    aaaaGCCCTGTCCCGAGGAAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAg  <  1:334574/151‑1 (MQ=255)                                                                                                                                                    aaaaGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGc    >  2:444641/1‑149 (MQ=255)                                                                                                                                                         |                                                                                                                                                  AGTGGCAAACGAACCGGAAACCGGCATATATGCAGCCAGTTCACCGAGACTGGTCATCAGGAAGTAAACCATCAGGCCAATCAGCATATACGAGAGCAATGCCCCGCCCGGACCT‑GCC‑TGAGAAATCGTTGCGCCAGAGGCAACAAAAAGACCTGTACCGATGGAACCGCCAATGGCAATCATCGTCAGGTGACGCGCCTTTAATTCACGGCGTAAGCCCGGCGCTTCTGTGGTTTTAGTTTCGGAAACCATACAAAAATGCTATCCATCTTAAAAATGAGGCGCGATTGTAGCAG  >  NC_000913/2248281‑2248576

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑