Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	44.9%	57.0 / 30.1	49	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (24/3);  new base A (0/22);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 5.18e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCT  >  NC_000913/29346‑29638                                                                                                                                                          |                                                                                                                                               tttAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAatat                                                                                                                                                >  1:149928/1‑151 (MQ=255)  ttAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAatat                                                                                                                                                >  2:670584/1‑150 (MQ=255)   tAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAAtata                                                                                                                                               <  2:606739/150‑1 (MQ=255)    aaTGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATaa                                                                                                                                              <  1:801400/150‑1 (MQ=255)       gTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATaaaaa                                                                                                                                           >  2:266246/1‑150 (MQ=255)         aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                        >  2:825199/1‑151 (MQ=255)                        ggTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTg                                                                                                                          >  1:186928/1‑150 (MQ=255)                         gTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAc                                                                                                                        >  2:549179/1‑151 (MQ=255)                           ccACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACtt                                                                                                                      >  2:261330/1‑151 (MQ=255)                                tttttCTCCTCTTTTTTATTTCATGAATTCTTTTTGCTCCGCAACCTTTTTCAAAAACAGGTT‑AGATAATTTTTTTGTCGCTTAACGCTT‑GTAAAA‑CTTGCATGAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAg                                                                                                                  <  1:144285/150‑1 (MQ=255)                                     cTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGccc                                                                                                             >  1:809929/1‑150 (MQ=255)                                      tGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGTTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGTCCa                                                                                                            >  1:328119/1‑150 (MQ=255)                                            ttttttttAAATCCATTCTTTTTGCGGCGAAAGCTTTTACCAAAAGAGTTT‑AGATTAT‑TTTTATTCCTTTAATTCCT‑TAAAAACCATGCATGCGCCCAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCat                                                                                                           <  1:278748/145‑1 (MQ=255)                                                tATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGa                                                                                                  >  2:561948/1‑150 (MQ=255)                                                tATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATATTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGAC‑TTTAGCGCCCATATCTCCAGAAt                                                                                                >  2:385642/1‑151 (MQ=255)                                                                    cggcgaAAGCTTTTTCCAGAACAGTTT‑AAATTTTTTTTTTTTCACTTAATCCCT‑ATAAAA‑CATGCATGGCCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAg                                                                                 <  1:762598/145‑1 (MQ=255)                                                                     ctgcgaaggcttttCCAAAAAAAGTTAAGATAATTTTTTTGTCGTTTAAGGCCT‑GAAAAA‑CATGAATGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                     <  1:71108/133‑1 (MQ=255)                                                                          atgcttttcCCAAAAAAGTTT‑AAATTATTTTTTTGTCGTTTAATCCCT‑AAAAAA‑ATTGCATGACCCAAAAAATAATAAAAAAACCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtc                                                                           <  1:252366/142‑1 (MQ=255)                                                                          aggctttttCAAGAACAGGTT‑AAAGAATTTTTTTGTCGTTTAATCCCT‑GTAAAA‑CATGAAGGACCCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgtc                                                                        <  2:401169/145‑1 (MQ=255)                                                                               ttttCAAGAACAGGTA‑AGATTTTCTTTTTGTCATTTATTGCCT‑TTAAAA‑CATGCATGACCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGt                                                                     <  2:449578/148‑1 (MQ=255)                                                                                tttCAAAAACAGTTA‑AGATGTTTTTTTTGTCTTTTAATGCTT‑TAAAAA‑CATGCATGCGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                                  <  2:269409/150‑1 (MQ=255)                                                                                     aGAACAGTTT‑AGATATTTTTTTTGTCTTTTAATGCTT‑ATAAAA‑AATGCATGAGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAt                                                             <  2:744006/150‑1 (MQ=255)                                                                                     aGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt                                                            >  1:199162/1‑151 (MQ=255)                                                                                     aGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt                                                            >  2:208181/1‑151 (MQ=255)                                                                                       aaCAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTg                                                          >  2:630130/1‑151 (MQ=255)                                                                                              taaaatgatTTTTTTGTCGTTTAATGCCT‑GAAAAA‑CATGCATGAGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAttt                                                           <  2:402752/140‑1 (MQ=255)                                                                                                    gatCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                              >  2:820095/1‑151 (MQ=255)                                                                                                     atCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                             >  1:251274/1‑151 (MQ=255)                                                                                                        tttttGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                          >  2:641019/1‑151 (MQ=255)                                                                                                        ttttcGCCGCTTAA‑GCCTAGAAAAA‑CAGCCAAAAGCCAAAAAAAAATAAAAAAAATGCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTa                                                <  2:709033/145‑1 (MQ=255)                                                                                                         tttttgccattAATCCCT‑GAAAAA‑AAGCCATGAGCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcat                                          <  2:7639/141‑1 (MQ=255)                                                                                                           ttGTCGCTTAATGCCT‑GTAAAA‑CATGCTTGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGtca                                                                   >  2:404894/1‑121 (MQ=255)                                                                                                                cgtttacggcctaaaaaa‑CATGCATGACCAAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTcatcat                                       <  1:103004/133‑1 (MQ=255)                                                                                                                  ttAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAAt                                >  2:490752/1‑151 (MQ=255)                                                                                                                    aaTGCCT‑GAAAAA‑CATTCATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTa                              <  2:80155/151‑1 (MQ=255)                                                                                                                      tGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                            >  1:109956/1‑151 (MQ=255)                                                                                                                        gtcttaaaaa‑CATGCGTGGGCCAAAAAAAAATAAAAAAAAGCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCTTTGTGaa                                 <  2:269395/139‑1 (MQ=255)                                                                                                                             tAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                       >  2:338302/1‑150 (MQ=255)                                                                                                                              aaaaaattgcatgAGCCACAAAATAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                       <  1:729050/143‑1 (MQ=255)                                                                                                                              aaaa‑CTTGCATGAACCAAAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCaa                      <  1:829446/150‑1 (MQ=255)                                                                                                                              aaaa‑CATGCATGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGc                        <  1:819483/148‑1 (MQ=255)                                                                                                                              aaaa‑CATGCATGACCAAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATg                         <  1:157608/147‑1 (MQ=255)                                                                                                                               aaa‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt                    >  2:738148/1‑151 (MQ=255)                                                                                                                                aa‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt                    >  1:130146/1‑150 (MQ=255)                                                                                                                                     tgcttaaGCCACAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaaa                 <  1:823653/143‑1 (MQ=255)                                                                                                                                             ccACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAat       >  2:4073/1‑151 (MQ=255)                                                                                                                                               aaaaaaaaATATAAAAATCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGaa        <  2:833163/146‑1 (MQ=255)                                                                                                                                               aaaaaaaaATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAatat     <  2:720709/149‑1 (MQ=255)                                                                                                                                               aaaaaaaaATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATaa                  <  2:723325/136‑1 (MQ=255)                                                                                                                                                caAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATAtt    >  1:576658/1‑151 (MQ=255)                                                                                                                                                  aaaaaaTAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtct  <  1:768187/151‑1 (MQ=255)                                                                                                                                                  aaaTAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtct  >  1:124665/1‑151 (MQ=255)                                                                                                                                                          |                                                                                                                                               TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT‑AGATGATCTTTTTGTCGCTTAATGCCT‑GTAAAA‑CATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCT  >  NC_000913/29346‑29638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑