Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,496	0	T	A	47.8%	43.0 / 30.4	46	intergenic (+301/‑155)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base T (20/4);  new base A (0/22);  total (20/26)
Fisher's exact test for biased strand distribution p-value = 1.94e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAG  >  NC_000913/29346‑29644                                                                                                                                                        |                                                                                                                                                     tttAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAatat                                                                                                                                                      <  1:543598/151‑1 (MQ=255)   tAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATaa                                                                                                                                                    <  1:319113/151‑1 (MQ=255)         aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATc                                                                                                                                              <  1:763824/151‑1 (MQ=255)                    aTTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAg                                                                                                                                   >  2:95967/1‑151 (MQ=255)                     tttGGTCCTTTTTTTTCTGTTCTTTTTTTTTTAATGAAATTTTTTTGCTGCGAAGGCGTTTACAAAAAAAGTTTAGATTATTTTTTTTTCGTTTAATCCC‑TAAAAAACATGCATGACCCAAAAAATAATAAAAAAAATCCCGCCATTAAGt                                                                                                                                  <  1:382551/151‑1 (MQ=255)                     tttGGTCCTTTTTTTTCTGCTCGTTTTTTTTTATTACAATTTTCTTGCTGCGCAAGCTTTTTCCAGAACAGTTAAAATGATTTTTTTGTCGCTTATTGCT‑TTAAAAACATGCTTGACCAAAAAAAAAATAAAAAAAATCCCGCCATTAAGt                                                                                                                                  <  1:471457/151‑1 (MQ=255)                       tGGTCCATTTTTTTCTGCTCTTTTTTATTTCATGCATTTTTCTTGCTGCGAAAGCTTTTTCAAAAACAGGTTAAATGATTTTTTTGTCGTTTATTGCC‑TGAAAAACATGCATGGGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTg                                                                                                                                <  1:349928/151‑1 (MQ=255)                             aCTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACtttt                                                                                                                          >  2:910062/1‑151 (MQ=255)                               ttttttCTGTGTTTTTTTTTTTCATGCATTTTTCTTGCGGCGAATGTTTTTTCCAAAATAGGTTAAATGTTTTTTTTGTCTATTAATGCC‑TATAAAACATGCATGGGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAg                                                                                                                        <  2:747921/151‑1 (MQ=255)                               ttttttCTGCTCTTTTTTTTTTAATCCATTCTTTTTCCTGCAAAAGCTTTTTCAAAAACAGGTTAGTAAATTTTTTTGTCGTTAAATCCC‑TTAAAAATATACATGGCCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAg                                                                                                                        <  1:212870/151‑1 (MQ=255)                               tttttgCTGCTCTTTTTTATTTCATGAATTTTTCTTGCGGCGAATGCGTTTCCAAGAACAGGTTAGATGATTTTTTTGTCGTTTAATCCC‑TGAAAAACTTGCATGACCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAg                                                                                                                        <  1:363195/151‑1 (MQ=255)                                  tttCTGCTCTTTTTTTTTTAATGAATTTTTTTTGCTGCGAAAGCGTTTTCAAAAACAGTTAAAATAATTTTTTTTTCGCTTAATGCC‑TGAAAAACATGCATGAACCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAgcgc                                                                                                                     <  2:547763/151‑1 (MQ=255)                                         tatgttttttttCATGCAATTTTTTTCCTCCACAATCTTTTTAAAGAAGATTTGAAAGAATTTTTGTGACTTTAAATGCC‑GAAAAAACAGGCAAGGTACAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtc                                                                                                              <  1:539571/147‑1 (MQ=255)                                            ttttttttTCATGAAATTTTCTTGCTGCGCAAGCGTTTTACAGAACAGGTTAAATGATTTTTTTGTCGCTTAAGGCC‑TGTAAAACATGACTGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                                           <  2:334669/151‑1 (MQ=255)                                            tttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATAtctc                                                                                                            >  2:814654/1‑150 (MQ=255)                                               ttATTTCATGCATGTTTTTTGGTGCGAAAGTGTTTACAAGAACAGGTAAGATGATCTTTTTGTCGCTTAATCCG‑TGAAAAACAGGCATAACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGa                                                                                                        <  1:814375/151‑1 (MQ=255)                                                tATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACCGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGaa                                                                                                       >  1:773380/1‑151 (MQ=255)                                                        gCAATTTTTTTGCTGCGAAAGCTTTTTAAAAAACGGGTTAGATGATTTTTTTTTCGTTTAATGCC‑TGAAAAACATGCATGACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATgccgc                                                                                                 <  2:818413/149‑1 (MQ=255)                                                         cAATTTTTTTGCTGCGAAAGCTTTTTCAAAAAAGGGTAAGATGATTTTTTTTTCTCTTAATGCC‑TTAAAAACTTGGATGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGccgccg                                                                                               <  2:755486/150‑1 (MQ=255)                                                         cAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGt                                                                                              >  2:909789/1‑151 (MQ=255)                                                           aTCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGttt                                                                                            >  1:676022/1‑151 (MQ=255)                                                             cttcttGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTg                                                                                           >  2:14111/1‑150 (MQ=255)                                                                                 ttCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCa                                                                      >  1:134365/1‑151 (MQ=255)                                                                                  tcaaaaaaggttaaaatgatTTTTTTCTCGTTAAATGCC‑TGAAAAACATGCAGGAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAg                                                                     <  2:943053/136‑1 (MQ=255)                                                                                      gAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAttt                                                                 >  1:633283/1‑151 (MQ=255)                                                                                                 ataatttttttGTC‑ATTAAAGCCTTGAAAAACTTGCAGGACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGAtt                                                        <  1:501364/143‑1 (MQ=255)                                                                                                    attttttttCCGCTAAATCCC‑TGAAAAAAATGCATGACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                   <  2:468196/148‑1 (MQ=255)                                                                                                    atttttttGTCTCTAAATGCT‑GTTAAAACATGAATGAGCCAAAAAAAAAAATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                   <  1:95957/148‑1 (MQ=255)                                                                                                    atCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGt                                                   >  2:935813/1‑151 (MQ=255)                                                                                                              cGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgtg                                         >  1:30240/1‑151 (MQ=255)                                                                                                              cGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgtg                                         >  2:59941/1‑151 (MQ=255)                                                                                                              cGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtgtg                                         >  2:565970/1‑151 (MQ=255)                                                                                                               gCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGa                                        >  1:202450/1‑151 (MQ=255)                                                                                                                cTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGaa                                       >  1:749726/1‑151 (MQ=255)                                                                                                                cTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGaa                                       >  1:1035493/1‑151 (MQ=255)                                                                                                                     tGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                  >  2:560120/1‑151 (MQ=255)                                                                                                                      tccctaaaaaaCATGCATGCCCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                                  <  2:467861/144‑1 (MQ=255)                                                                                                                        cctaaaaacCATGCATGACCAAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAata                                 <  2:747951/145‑1 (MQ=255)                                                                                                                        c‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATg                               >  2:726953/1‑151 (MQ=255)                                                                                                                          ttaaaaaCATGCAGGCCCCAAAAAATAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGc                              <  2:104577/148‑1 (MQ=255)                                                                                                                           gTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCa                             >  2:461093/1‑151 (MQ=255)                                                                                                                                  tggcatgAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                      <  1:352376/149‑1 (MQ=255)                                                                                                                                    gaagggcccAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAag                      <  2:630059/142‑1 (MQ=255)                                                                                                                                             aaaaaaaaaaaaaaaaaaTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAatat           <  2:669631/149‑1 (MQ=255)                                                                                                                                             aaaaaaTAATAAAAAAATCCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAatat           <  1:909473/149‑1 (MQ=255)                                                                                                                                               aaaaTAATAAAAAAATTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATtc         <  1:119970/151‑1 (MQ=255)                                                                                                                                                aaaTAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATAtt          >  2:248736/1‑149 (MQ=255)                                                                                                                                                    aataAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTgg    <  2:682739/151‑1 (MQ=255)                                                                                                                                                      aataAAAACTCCCGCCATTAAGTTGGCTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTTATTTACTTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAg  <  1:610362/150‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                     TTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCC‑TGTAAAACATGCATGAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGTGAATATTCTCTGGAG  >  NC_000913/29346‑29644

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑