Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,222,596	0	G	A	44.4%	49.9 / 39.6	54	F13F (TTC→TTT)	ymgD	uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (27/3);  new base A (0/24);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 4.17e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCATTACCCATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTGAC  >  NC_000913/1222453‑1222739                                                                                                                                                |                                                                                                                                                cTGGCATTACCCATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAaaaca                                                                                                                                           >  2:681182/1‑150 (MQ=255) cTGGCATTACCCATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAaaaca                                                                                                                                           >  1:186625/1‑150 (MQ=255)  tGGCATTACCCATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAaaacaa                                                                                                                                          >  1:318915/1‑150 (MQ=255)            cattaccGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGcc                                                                                                                               <  1:14637/151‑1 (MQ=255)               taccGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAg                                                                                                                             <  1:588970/150‑1 (MQ=255)                     aacatTTTCTGCAACCTGTGCGTTGTCATTTTTTGCTTTTTCGTTGGCTTCTGCGAAATTAATATAGTTTTCTGACGACAAACCTTTTTTAATTTTGTAGCCCGGCGCCCAGGTCATGGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCa                                                                                                                      <  1:738699/151‑1 (MQ=255)                                cAACCTGTGCGCTGTCAGTTTTTGCCTTTTCGTTGGCTTCTGCGAAAGTAATATAGGTTTCTGCCGGCAAACCTTTTTTAATTTTGTAGTCCTGCCCCCAGGTCTTTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTtca                                                                                                            <  2:634375/150‑1 (MQ=255)                                 acccTTTGCGCTTTCAGTTTTTGCTTTTTCTTTGGCTTCTGCGCAAGAAATATAGTTTTCTGACGCCACCCCTTTTTAATTATTGTATCCCGGCGCCCATTTAATTGGAGAAAAAACAAACGGGCCCGCCAGTAAAGCAAATTTTTtcat                                                                                                           <  1:857585/148‑1 (MQ=255)                                  aCCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTtcatc                                                                                                          >  1:97006/1‑150 (MQ=255)                                      gggcgaTGTCAGTTTTGGCCATTTCGTTGTTTTCTGCGCAATAAATAATGGTTTCTGACGGCAACCTGTTTTTAATATTGTAGCCCTCCCCCCAGGTCATGGGTGCAAAAACAAACAGCCCCGCCAGTAAAGCAAATTTTTtcatca                                                                                                         <  2:482876/145‑1 (MQ=255)                                          gcTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCt                                                                                                 >  2:63110/1‑151 (MQ=255)                                            tGTCATTTTTTGCCTTTTCGTTGGCTTCTGCGAAAGAAATATAGTTTTCGGACGGAAACCCTTTTTTAATATTGTAGCCCGGCGCCCAGGTCTTTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTc                                                                                                   <  1:440879/147‑1 (MQ=255)                                            tGTCATTTTTTCCCATTTCTTTGGTTTCTGCACAAATAATATAGTTTTGTGTCGGAAACCCTTTTTAAATTTTGTGGCCCTGCGCCCAGTTTTTTGGGGCAAAAAAAAACCGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCt                                                                                                 <  1:743007/149‑1 (MQ=255)                                            tGTCAGTTTTTGCCTTTTCGTTGGTTTCTGCGAAAGTAATATAGTTTTCTGACGGAAACCCTTTTTTAATATTGTAGCCCTGCCCCCAGGTTTTTGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTc                                                                                                   <  1:142166/147‑1 (MQ=255)                                                  tttttGCCTTTTCTTTGTTTTCTGCGCAAGTAATATAGTTTTCTGACGGAAACCCTTTTTAAATATTGTAGTCCTGCGCCCAGTTTTTTGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTAt                                                                                              <  1:141494/146‑1 (MQ=255)                                                  tttttGCCATTTCTTTGGTTTCTGCGAAAGTAATATAGGTTTCTGACGGCAACCCTTTTTTAATTTTTTGTCCCTGCCCCCAGGTCATTGGTGCAAAAACAACCAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTa                                                                                               <  2:165635/145‑1 (MQ=255)                                                    tttGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAttt                                                                                       >  1:718332/1‑151 (MQ=255)                                                     ttGCCTTTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAACCCTTTTTTAATATTGTAGTCCGGCGCCCAGGTCATTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCAttt                                                                                       <  2:212449/150‑1 (MQ=255)                                                        ccttttCGTTGGTTTCTGCGAAAGTAATATGGGTTTCTGACGGCAACCCTTTTTTAATTTTGTAGTCCTGCCCCCAGTTTTTTGGTGCAAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTAc                                                                                    <  1:520960/147‑1 (MQ=255)                                                             tctttGGTTTTTGCACAAGAAATATAGTTTTTTCACGGAAACCCTTTTTAAATATTGTAGCCCTGCCCCCATTTTTTTGGGCAGAAAACAACCAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGa                                                                               <  1:265737/147‑1 (MQ=255)                                                             tCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGa                                                                               >  1:465874/1‑150 (MQ=255)                                                              cGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAAt                                                                             >  1:194874/1‑151 (MQ=255)                                                                  ggCGTCTGCGCATTTAATATAGTTTCCGGATGTCAAACCTTTTTTAATATGATCGTCCGGCCCCCCGGCGATTGGCGAAAAAACAAAACGGTCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGc                                                                          <  2:460667/150‑1 (MQ=255)                                                                    cTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGcacc                                                                       >  1:448183/1‑151 (MQ=255)                                                                          agcAAGAAAAAAAGTTTTCGGACGGCAAACCGTTTTTAATATTGAAGTCCAGCCCCAAGTTTATTGGGAAAAAAAAAAACAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGt                                                                 <  2:439323/150‑1 (MQ=255)                                                                             aaatAATATAGGTTTCAAACGTGACGCGTTTTTTAATTTATTTCTCCACCGCCAAGATCATGGGCGAAAAAACAAACCTCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCCCCCg                                                                  <  1:1081293/144‑1 (MQ=255)                                                                             aaGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTAcc                                                              >  1:371353/1‑151 (MQ=255)                                                                                  atatAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCa                                                          >  2:593858/1‑150 (MQ=255)                                                                                            cTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCAcc                                               >  2:276243/1‑151 (MQ=255)                                                                                            cTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCAcc                                               >  1:41489/1‑151 (MQ=255)                                                                                             tGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCt                                              >  2:771120/1‑151 (MQ=255)                                                                                                    aacctttttttAATTTTTTAGCCCCGCCCCCAGTTTTTTGGTCCAAAAAAAACCGGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCttt                                            <  1:1050767/140‑1 (MQ=255)                                                                                                      cctttttttAATTTTGTACTCCTGCCCCCAGGTCTTTGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGcc                                     <  2:238434/147‑1 (MQ=255)                                                                                                       ctttttttAATTTTGTACCCCTCCCCCCGGGTCTTTGGTGCAAAAACAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGc                                      <  2:537340/146‑1 (MQ=255)                                                                                                         tttttaAATTTTGTAGCCCTGCCCCCGGTTCTTTGGTGCAAAAAAAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGccc                                    <  1:224542/148‑1 (MQ=255)                                                                                                          tttttAATTTTTTCGCCCTGCCCCCAGTTCATGGGGGAAAAAACAACCGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCt                                  <  1:1006150/150‑1 (MQ=255)                                                                                                           ttttAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTc                                >  1:907710/1‑151 (MQ=255)                                                                                                            tttAATTTTGTAGCCCTGCGCCCAGGTCATGGGTGCAAAAAAAAACGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTc                                <  2:930384/150‑1 (MQ=255)                                                                                                              tAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCg                               >  1:86637/1‑149 (MQ=255)                                                                                                                atatTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGc                           >  1:551733/1‑151 (MQ=255)                                                                                                                  atTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGcc                          >  1:676313/1‑150 (MQ=255)                                                                                                                  atTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGcc                          >  1:910698/1‑150 (MQ=255)                                                                                                                         tCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCgg                  >  2:662817/1‑151 (MQ=255)                                                                                                                           cTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTc                >  2:1099926/1‑151 (MQ=255)                                                                                                                              cgcCCAGGTCTTTGGTCAAAAAACAACCAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCa               <  1:105170/149‑1 (MQ=255)                                                                                                                               gcCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTc                >  1:541366/1‑147 (MQ=255)                                                                                                                               ccccAGTTCATTGGTGCAAAAACAACCGGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGaa            <  1:70637/150‑1 (MQ=255)                                                                                                                                cccGGGTCATTGGTGCAAAAAAAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAAc           <  2:1050676/151‑1 (MQ=255)                                                                                                                                   aGGTCCTTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGcc        >  2:1096428/1‑151 (MQ=255)                                                                                                                                      tCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGt     >  1:761431/1‑151 (MQ=255)                                                                                                                                       cATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTg    >  1:257895/1‑151 (MQ=255)                                                                                                                                         ttGGTGCAAAAAAAACCAGCCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTGa   <  2:591313/150‑1 (MQ=255)                                                                                                                                          tGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTGAc  >  1:149309/1‑150 (MQ=255)                                                                                                                                          tGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTGAc  >  2:680383/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                CTGGCATTACCCATTACCGCAACAATTTCTGCAACCTGTGCGCTGTCAGTTTTTGCCATTTCGTTGGCTTCTGCGCAAGTAATATAGGTTTCTGACGGCAAACCGTTTTTAATATTGTAGTCCTGCGCCCAGGTCATTGGTGCGAAAACAAACAGGCCCGCCAGTAAAGCAAATTTTTTCATCATCATTCCTTATTTCATTTTACCCAGAATTGCACCACCCGTACCGCCAATCACGGCACCTTTAATCGCCCCTTCGAGGCCATTGCCGGTCAGAACGCCAGTGAC  >  NC_000913/1222453‑1222739

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑