Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	46.2%	53.5 / 29.6	52	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (20/8);  new base A (0/24);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 3.42e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAG  >  NC_000913/29349‑29644                                                                                                                                                       |                                                                                                                                                     aaTGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATaaa                                                                                                                                                   <  1:806495/151‑1 (MQ=255)   tGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATaaaa                                                                                                                                                  >  1:867734/1‑150 (MQ=255)     tAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAAt                                                                                                                                               >  2:494076/1‑151 (MQ=255)            tGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGcc                                                                                                                                         <  1:790199/150‑1 (MQ=255)                   ttGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGtt                                                                                                                                 >  2:139972/1‑151 (MQ=255)                      gTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                              >  2:4243/1‑151 (MQ=255)                        ccttttttttCTTCTCTTTTTTATTTCATCCATTTTTTTTGCGGGGAAAGCTTTTAACAG‑AACGGA‑TTAAATTATTTTTTTTTCGATAAATCCTTTAAAAA‑CAGGCTGGAGCCACAAAAAAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                              <  1:653392/145‑1 (MQ=255)                            ttttttCTGCTCTTTTTTATTTCATGCATTCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGTTTAATGCCTGTAAAA‑CAGGCATGAGCCACAAAATAATAAAAAAAATCCCGCCATTAAGTTGACttt                                                                                                                           <  2:640783/148‑1 (MQ=255)                             tttttCTTCTTTTTTTTATTTCATGAAATCTTCTTGCTGCACAAGCTTTTTCAAG‑AACAGG‑TTAGATAATTTTTTTGTCTCTTAATGCCTGTAAAA‑CATGCATGAGCCAAAAAATAATATAAAAAACCCCGCCATTAAGTTGACTTTTAg                                                                                                                        <  1:323554/150‑1 (MQ=255)                                      tCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                              >  2:552416/1‑151 (MQ=255)                                           tttATTTCATGAATTCTTCTTGCGGCACAAGTTTTTTCCAG‑AACAGG‑TTAGATAATTTTTTTGTCTTTTAATGCCTATAAAA‑AATTTATTAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCa                                                                                                          <  1:583427/150‑1 (MQ=255)                                                   aTGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgc                                                                                                 >  1:573458/1‑151 (MQ=255)                                                   aTGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgc                                                                                                 >  1:659477/1‑151 (MQ=255)                                                    tacAATCTTTTTGCTGCCAAAGCTTTTTCCAA‑AAGAGT‑TAAAATAATTTTTTTGTCACTTAATGCCTGAAAAA‑CATGCATGATCCACAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccg                                                                                                  <  1:551794/147‑1 (MQ=255)                                                          cttcttGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGc                                                                                          >  1:731979/1‑151 (MQ=255)                                                             cttGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                                         >  2:426686/1‑149 (MQ=255)                                                                gctgcGCAAGCGTTTTCAAG‑AACGGT‑TTAGATATTTTTTTTTTCTTTTAATGCCTGAAAAA‑CATGCAGGAGCCACAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGa                                                                                      <  1:548791/149‑1 (MQ=255)                                                                    cgcAGGCGTTTTCAAA‑ACCGGG‑TTAGATTTTCTTTTTGCGGATAAATGCCTGAAAAA‑CATGAATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                                 <  2:676629/150‑1 (MQ=255)                                                                     caaaagcttttCCAA‑AACAGGTTTAATTTATTTTTTGGCAACTTAAGGCCTATAAAC‑CATGCGGGGGCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGccgccg                                                                                               <  1:787776/129‑1 (MQ=255)                                                                       atgttttttCCAG‑AAAATG‑TTAGATGATTTTTTTGTCTTTTAATTCCTTAAAAA‑CATGATTGCCCAAAAAAATAATATAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtcg                                                                             <  1:580783/146‑1 (MQ=255)                                                                       aaGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtcg                                                                             >  2:348664/1‑151 (MQ=255)                                                                            ttttCCAAAAACAGT‑TTAAATGTTTTTTTTGCCGTTTAATGCC‑GTAAAACCTTCCAGGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCgg                                                                            <  2:287762/148‑1 (MQ=255)                                                                             tttCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                                       >  2:694566/1‑151 (MQ=255)                                                                              ttCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                                       >  1:676130/1‑150 (MQ=255)                                                                               gccAG‑AACAGG‑TTAAAAGTTTTTTTTGAGGCTAAATGCTGAAAAAA‑CATCCAGGGGCAACAAAATAATAAAAAAAAGCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                      <  2:891084/149‑1 (MQ=255)                                                                                   aaaatggg‑TTAGATGTTTTTTTGGTCTCTTAATGCTTGTAAAA‑CATGCTTGAGCCAAAAAAAAAAATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAt                                                                   <  1:653637/144‑1 (MQ=255)                                                                                      aCAGG‑TTATATGATTTTTTTGTCTATAAATCCATAAAAAA‑AAGGCATAACACAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCGCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                               <  1:817984/151‑1 (MQ=255)                                                                                      aCAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTGGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                               >  2:481278/1‑151 (MQ=255)                                                                                          gtttAGATGATTTTTTTGTCGCTTAATGCCTGAAAAA‑CATGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCa                                                              <  2:16772/147‑1 (MQ=255)                                                                                                atgatCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAttt                                                       >  2:84535/1‑150 (MQ=255)                                                                                                atattCTTTTTGGCGCTTATTCCCTAAAAAC‑CGTGAGTGACCCAAAAAAAAATAAAAAAATTGCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                        <  1:177674/145‑1 (MQ=255)                                                                                                 tgttttttttGCCGTTAAATCCTTGAAAAA‑CATGCAGGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTa                                                      <  2:638230/145‑1 (MQ=255)                                                                                                  gatCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                                    >  2:19946/1‑151 (MQ=255)                                                                                                    tttttttGTCGCTTAATGCCTATAAAA‑CATGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAttt                                                       <  2:547286/144‑1 (MQ=255)                                                                                                    tCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                                  >  1:160732/1‑151 (MQ=255)                                                                                                       ttttGTCGATTAATCCTTTAAAAA‑CAGGCATGACCAACAAAAAAATTAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                                <  1:166084/150‑1 (MQ=255)                                                                                                       ttttGTCACTTAATCCCTGAAAAA‑CATGCATGAGCAACAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                                <  1:229513/150‑1 (MQ=255)                                                                                                                ttATTGCCTATAAAA‑AATCAATGCCCAAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGaa                                       <  1:530278/150‑1 (MQ=255)                                                                                                                 tAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAAtt                                     >  2:285346/1‑151 (MQ=255)                                                                                                                  aaTGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCACCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTa                                    <  1:355043/151‑1 (MQ=255)                                                                                                                     gCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                  >  2:582646/1‑150 (MQ=255)                                                                                                                      ccTGAAAAA‑CATGCATGAGCAAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAatat                                <  1:520618/151‑1 (MQ=255)                                                                                                                        tgaaaaa‑CATGCTGGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                                 <  1:652596/145‑1 (MQ=255)                                                                                                                          aaaaa‑CATGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAatat                                <  2:56610/146‑1 (MQ=255)                                                                                                                           aaaa‑CATGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                             <  2:397551/149‑1 (MQ=255)                                                                                                                           aaaa‑CAGGCATGACCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCaaa                           <  1:139942/151‑1 (MQ=255)                                                                                                                            aaa‑CAAGCACGCGCCAAAAAAGAATATAAAAAATCCCGCCATTAAGTGGACGTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAGTGATTTACGTCATCATTGTGAATTGata                                 <  1:212699/144‑1 (MQ=255)                                                                                                                                 atgcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa                        >  1:366683/1‑149 (MQ=255)                                                                                                                                   gcatgAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg                    >  2:687621/1‑151 (MQ=255)                                                                                                                                       gAGCAAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaaa                       <  2:641522/144‑1 (MQ=255)                                                                                                                                                   aataAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTg     <  2:837038/150‑1 (MQ=255)                                                                                                                                                   aataAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg    <  1:751347/151‑1 (MQ=255)                                                                                                                                                     tataAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg    >  2:415110/1‑149 (MQ=255)                                                                                                                                                      ataAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAg  <  1:678956/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                     AATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAG‑AACAGG‑TTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAG  >  NC_000913/29349‑29644

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: ‑