Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	49.0%	43.3 / 36.0	51	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (23/3);  new base A (0/25);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.47e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG  >  NC_000913/29349‑29642                                                                                                                                                        |                                                                                                                                                   aaTGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCTTTTTTATTTCATGCAATCTTCTTGCTGCCCAAGCGTTTCCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGACCCACAAAATAATATaat                                                                                                                                                 <  2:187112/151‑2 (MQ=255)    gttaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATaaaaa                                                                                                                                               >  1:657746/4‑150 (MQ=255)     tAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAAt                                                                                                                                             >  2:773162/1‑151 (MQ=255)         ttttGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCg                                                                                                                                         >  2:880846/1‑151 (MQ=255)             gACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCAt                                                                                                                                     >  1:40347/1‑151 (MQ=255)              aCCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCAtt                                                                                                                                    >  2:15010/1‑151 (MQ=255)                    tGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTg                                                                                                                              >  2:631693/1‑151 (MQ=255)                      gTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                            >  1:816724/1‑151 (MQ=255)                      gTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                            >  1:439322/1‑151 (MQ=255)                           tttttttCTGCTCTTTTTTATTCATTGCATTCTTCTTGTTGCACAAGCTTTTTCA‑AAAA‑CAGGTT‑AGATGATTTTTTTGCCTTTTAATGCCTGAAAAACA‑TCCATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                                        <  1:58940/149‑1 (MQ=255)                                    gCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCat                                                                                                               >  2:146073/1‑150 (MQ=255)                                           ttttttacttGCAATCTTCTTCCGACG‑AAGGCTTTTCC‑AAAATCAGTTA‑AGAGTATTTTTTTTTCATTTAAT‑CCTGTAAAAAATTGATTGACCCCAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCa                                                                                                        <  2:689863/141‑1 (MQ=255)                                            ttATTTCATGCATTTTTTTTCCTCCGAAACCGTTTCCC‑AGAA‑AAGGTT‑ATATTATTTTTTTGTCCCTAATTCCCTGAAAAACT‑TGCATGAGCAAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAg                                                                                                       <  2:811531/150‑1 (MQ=255)                                                  cATGCATTCTTCTTGCTGCGCAAGCTTTTCCC‑AGAA‑CAGGTT‑AGATGATTTTTTTGTCGTTTAATGCCTGAAAAACA‑TGCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgc                                                                                                  <  1:68463/149‑1 (MQ=255)                                                    tGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgcc                                                                                              >  1:394749/1‑151 (MQ=255)                                                       aaTCTTCTTGCTGCGCAAGCTTTTTCA‑AGAA‑CAGGTT‑AGATGATTTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgcc                                                                                              <  1:550360/148‑1 (MQ=255)                                                        aTCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                          >  1:472859/1‑151 (MQ=255)                                                           ttcttGTTGCACAGGCTTTTCCA‑AGAA‑CGGTTT‑AAATTATTTTTTTGCCTCTAAATACTTTAAAAACA‑TGAAGGGCCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGtt                                                                                           <  1:522495/147‑1 (MQ=255)                                                           ttcttGCTGCGCAAGCTTTTTCA‑AGAA‑TAGTTA‑AGTTTATTTTTTTGTCGTTAAATGCCTGAAAAACA‑TGCAGGAGCCAAAAAAAAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccg                                                                                                <  1:501493/142‑1 (MQ=255)                                                            tcttGCTGCGAAAGC‑TTTTCC‑AAAA‑ACGGTTAAAATTTTTTTTTTTTCTTTTAATGCTTAAAAAACA‑TGAATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                         <  2:819956/148‑1 (MQ=255)                                                              ttcctgcGCAAGCTTTTCCC‑AAAA‑CAGGTT‑AGATGATTTTTTTGTCGTTTAATCCTTGAAAAACA‑TGCATGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGc                                                                                        <  1:809194/144‑1 (MQ=255)                                                                 ctgcACAAGCTTTTCCC‑AGAA‑CGGTTA‑AGATGATTTTTTTGTCGTTAAATGCCTGAAAAACA‑TCCATGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCa                                                                                      <  1:843467/146‑1 (MQ=255)                                                                  tgcGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAAtt                                                                                >  1:449547/1‑151 (MQ=255)                                                                   gcgcAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                               >  1:494663/1‑151 (MQ=255)                                                                    cgaaaGCTTTTTCA‑AAAA‑CAGGTT‑AGATGATTTTTTTTTCGTTTAATGCTTAAAAAACA‑TGCATGAGCCAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAAt                                                                                 <  2:381053/145‑1 (MQ=255)                                                                       aggctttttCA‑AAAA‑CAGGTT‑AGATTTTTTTTTTGTCTTTTAATCCTTAAAAAACA‑TGAATGACCAAAAAAAAAAAAAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtc                                                                            <  2:570214/145‑1 (MQ=255)                                                                            ttttCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTa                                                                        >  1:859010/1‑149 (MQ=255)                                                                             tttCCAAGAA‑CAGGTA‑AGATGATTTTTTTGTCGCTTAATGCCTGAAAAACA‑TGCAGGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTaa                                                                       <  1:461663/150‑1 (MQ=255)                                                                             tttCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                                      >  1:193240/1‑150 (MQ=255)                                                                                tcccaaaaagggTT‑AGATGATTTTTTTGTCGCTTAATGCTTAAAAAAAA‑TGAAGGAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                                     <  1:278690/140‑1 (MQ=255)                                                                                   aGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt                                                                >  2:480255/1‑151 (MQ=255)                                                                                      a‑CAGTTT‑AGATGTTTTTTTTGTCTTTTAAGGCCTGAAAAACA‑TGAATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGc                                                             <  1:861089/151‑1 (MQ=255)                                                                                         aGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAt                                                           >  2:46129/1‑151 (MQ=255)                                                                                                  tgttttttttCTCGCTAAATCCTTTAAAAACA‑GGCATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAt                                                       <  2:664897/142‑1 (MQ=255)                                                                                                     ttttttttTCGTTTAAGCCCTAAAAAACA‑TGCATGACCCAAAAAATAATAAAAAAACTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                                  <  2:449561/147‑1 (MQ=255)                                                                                                      cTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                                >  1:519084/1‑150 (MQ=255)                                                                                                      cTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                                >  2:566640/1‑150 (MQ=255)                                                                                                       ttttttTCCTTTAATCCCTTAAAAACT‑TGCATGCCCAAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                 <  2:33467/148‑1 (MQ=255)                                                                                                        ttttttCGCTTAATCCCTATAAAACA‑TGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtc                                                <  1:189468/148‑1 (MQ=255)                                                                                                            gTCGTTTAAGGCCTGTAAAACA‑TGCAGGAGCAAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCAtt                                          <  2:137151/150‑1 (MQ=255)                                                                                                            gTCACTTAATGCCTGAAAAACT‑TGCATGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTcatcat                                           <  1:551707/149‑1 (MQ=255)                                                                                                                     tGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                >  1:477321/1‑151 (MQ=255)                                                                                                                      gCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                >  1:751930/1‑150 (MQ=255)                                                                                                                            aaaaCA‑TGCATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCaa                          <  1:862221/150‑1 (MQ=255)                                                                                                                               aCA‑TGCATGACCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa                      <  1:443802/151‑1 (MQ=255)                                                                                                                                   tgcaggAACCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATa                       <  2:157754/147‑1 (MQ=255)                                                                                                                                      atgACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaaa                     <  1:752781/146‑1 (MQ=255)                                                                                                                                       tgaccaaaaaaaaaATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgag                <  1:808631/142‑1 (MQ=255)                                                                                                                                         aGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagtg              >  2:227492/1‑150 (MQ=255)                                                                                                                                           ccACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat           >  1:594779/1‑151 (MQ=255)                                                                                                                                                  ataataAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTctct    <  1:562594/151‑1 (MQ=255)                                                                                                                                                      tataAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg  >  2:168288/1‑149 (MQ=255)                                                                                                                                                        |                                                                                                                                                   AATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAA‑CAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCTGTAAAACA‑TGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGG  >  NC_000913/29349‑29642

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: ‑