Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	29,486	0	C	A	43.2%	54.5 / 27.1	44	intergenic (+291/‑165)	dapB/carA	dihydrodipicolinate reductase/carbamoyl phosphate synthetase small subunit, glutamine amidotransferase
Reads supporting (aligned to +/- strand):  ref base C (19/6);  new base A (0/19);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.62e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTTTTGTTGTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGT  >  NC_000913/29336‑29629                                                                                                                                                         |                                                                                                                                                tttttGTTGTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCcac                                                                                                                                                 >  1:413224/1‑151 (MQ=255)       ttgttTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAaat                                                                                                                                            >  1:487412/1‑150 (MQ=255)             tAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAAtata                                                                                                                                      >  1:72502/1‑150 (MQ=255)              attGTAAATTTTG‑CCATTTTGTCCAACTTTTTCCTCCCCTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATaaaa                                                                                                                                   <  1:573403/149‑1 (MQ=255)                  tAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAAt                                                                                                                                >  1:119142/1‑151 (MQ=255)                   aaaTTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTGCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAAt                                                                                                                                <  1:50072/150‑1 (MQ=255)                          gACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCAt                                                                                                                        >  2:15021/1‑151 (MQ=255)                             cATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTa                                                                                                                      >  1:297270/1‑150 (MQ=255)                                 tGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTg                                                                                                                 >  1:468412/1‑151 (MQ=255)                                          tttttCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAgc                                                                                                        >  1:333295/1‑151 (MQ=255)                                             ttCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGcc                                                                                                     >  1:411903/1‑151 (MQ=255)                                                   tCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCTTTTTCC‑AGAACAGTTTAGATGATTTTTTTGTCGCTTAATGCCTGAAAAACATGCAT‑GAGCCACAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGccc                                                                                                    <  1:42444/146‑1 (MQ=255)                                                      tttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                            >  1:369179/1‑151 (MQ=255)                                                       ttttATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTcc                                                                                            >  1:230547/1‑150 (MQ=255)                                                        tttATTTCATGCATTTTTTTTGCTGCGAAAGCTTTTTCC‑AAAACGGTTTAAATAATTTTTTTGTCGTTTAATGCCTGAAAAACATGAAG‑GACCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCa                                                                                           <  1:187196/150‑1 (MQ=255)                                                          tATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGACACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTATTAGCGCCCATATCTCCAGa                                                                                         >  2:227790/1‑150 (MQ=255)                                                                           ttGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGcc                                                                          >  2:238081/1‑148 (MQ=255)                                                                           ttGCTGCGAAAGCTTTTTCC‑AAAACAGTTTAGATGTTTTTTTTGTCGTTTAATCCCTGAAAAACATGCAT‑GAGCCAAAAAATAATATAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGccgccg                                                                                <  1:497229/142‑1 (MQ=255)                                                                            tgctgcGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGa                                                                       >  1:539449/1‑150 (MQ=255)                                                                                  gcAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATtcgt                                                                >  1:70021/1‑151 (MQ=255)                                                                                     aGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCgg                                                             >  1:427497/1‑151 (MQ=255)                                                                                       gcttttCCAAGAACAGTTTAGATGATTTTTTTGTCGCTTAATGCCTGAAAAACATGCAT‑GACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCgg                                                             <  1:169439/148‑1 (MQ=255)                                                                                         ttttCA‑AAAAAAGGTTAGATTATTTTTTTTTCACTAAATCCCTTAAAAACATGCAT‑GACCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTa                                                           <  2:8817/149‑1 (MQ=255)                                                                                          tttCC‑AGAACAGTTTAGATTTTCTTTTTGGCGCTTAATCCCTGAAAAACATGCAT‑GAGCCAAAAAAAAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                         <  1:506966/150‑1 (MQ=255)                                                                                          tttCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGACATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAg                                                         <  1:327900/150‑1 (MQ=255)                                                                                              c‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGc                                                        >  2:320927/1‑147 (MQ=255)                                                                                                aaaaaaGGTTAAATGTTTTTTTTTTCGTTAAATGCCTGAAAAAAAGGAAT‑GACCCAAAAAAAAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAg                                                      <  2:519868/143‑1 (MQ=255)                                                                                                aaaaCAGTTTAAATAATTTTTTTGTCG‑TTAAATCCTTTAAAACCAGGATGGACCCAAAAAAAAAAAAAAAAAAGCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAt                                                    <  2:206963/148‑1 (MQ=255)                                                                                                aGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGAtt                                                   >  1:258870/1‑151 (MQ=255)                                                                                                      gttaaaaatatttttttGTCTCTAAATGCTTGAAAAACATGAAT‑GAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAt                                              <  2:332062/138‑1 (MQ=255)                                                                                                        ttAGATGATTTTTTTTTCGCTTAATGCCTATAAAACATGCAT‑GAGCCACAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                             <  2:405915/149‑1 (MQ=255)                                                                                                             tgatTTTTTTGTCTCTTAATCCCTGAAAAACATGAAT‑GACCCAAAAAATAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCAtt                                             <  2:561919/144‑1 (MQ=255)                                                                                                              gttCTTTTTGTCGTTAAATGCCTGTAAAACATGCAT‑GACCCAAAAAATAAAATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                     <  2:422612/149‑1 (MQ=255)                                                                                                                 ttttttGTCGATTAATCCCTTAAAAACATGCAG‑GAGCCACAAAAAAAAAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACg                                     <  2:620989/147‑1 (MQ=255)                                                                                                                     ttttcttttAATGCCTGAAAAAAATGCAT‑GAGCCAAAAAATAATAAAAAAAACCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGtcatca                               <  2:119115/143‑1 (MQ=255)                                                                                                                         cgtttAATGCCTGAAAACCATGCAT‑GAGCCAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATtg                            <  2:165040/146‑1 (MQ=255)                                                                                                                                 gCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAat                   >  1:587962/1‑150 (MQ=255)                                                                                                                                    tgaaaaaCATGCAT‑GACCCAAAAAATAAAATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTaa                    <  1:590805/143‑1 (MQ=255)                                                                                                                                        aaaCATGCAT‑GACCAAAAAAAAAATAAAAAAACTCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAAt           <  2:128216/151‑1 (MQ=255)                                                                                                                                               cat‑gAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg     >  1:17689/1‑150 (MQ=255)                                                                                                                                                   gacccAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg     <  1:533209/144‑1 (MQ=255)                                                                                                                                                    acccAAAAAAAAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgag   <  2:395503/146‑1 (MQ=255)                                                                                                                                                    aGCCAAAAAAAAAAAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATACCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagt  <  2:148031/149‑1 (MQ=255)                                                                                                                                                      ccAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtgagt  <  1:65536/147‑1 (MQ=255)                                                                                                                                                      ccAAAAAATAATAAAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAagtg     <  1:52419/144‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                TTTTTGTTGTTTTAATGTAAATTTTGACCATTTGGTCCACTTTTTTCTGCTCGTTTTTATTTCATGCAATCTTCTTGCTGCGCAAGCGTTTTCC‑AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCTGTAAAACATGCAT‑GAGCCACAAAATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTTACGTCATCATTGTGAATTAATATGCAAATAAAGTGAGT  >  NC_000913/29336‑29629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑