Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,159	0	G	A	46.0%	24.1 / 24.6	37	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (19/1);  new base A (0/17);  total (19/18)
Fisher's exact test for biased strand distribution p-value = 1.13e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5026‑5307                                                                                                                                       |                                                                                                                                                     aTTCATTATCTAAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTtc                                                                                                                                     >  1:637590/1‑151 (MQ=255)       tATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCg                                                                                                                               >  2:364107/1‑151 (MQ=255)        aTCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCg                                                                                                                               >  2:359652/1‑150 (MQ=255)                     cGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGat                                                                                                                 >  1:466229/1‑151 (MQ=255)                      gggTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGat                                                                                                                 >  1:402856/1‑150 (MQ=255)                        gTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                                                                              >  2:387380/1‑151 (MQ=255)                         tttGTTTTAATGCAGCCCGGTTTTTTTATGAAAAAATTAGGGAAAAAAATGACAGGAAAAAAGGAAAAA‑TTCCAAATAAATGCGTTAACTTAGAAATTAGGATTGGGGAAAATAAAAACCGCCGTTCTCATCGAGTAATCTcc                                                                                                                     <  1:77926/143‑1 (MQ=255)                         tttGCTTTAAGCGAGCCCGTTTTTTTTAAGAAAAAATTAT‑GAAAAAAAAGAAAGGGAAAAAGGAAAAACTTCACAATAAATGGGCTACCTAAGAGTTTAGAATTGGGGAAAACAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATc                                                                                                              <  1:155181/150‑1 (MQ=255)                                 tATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATa                                                                                                      >  1:578801/1‑150 (MQ=255)                                   ggCAGCCGGTTTTTTTTATAAAAAAATTAGGGAAAAAAATGAAAGGGAAAAAGGAAAAT‑TTCTCAATAAAGGGGTTATTTAAGAGATAGGGATGGCGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACg                                                                                                   <  1:270914/150‑1 (MQ=255)                                           tgttttttaATAAAAAAATATTGAAAAAAAATGAAAGGGAAAAAGGAGAAA‑TTCTAAATAATTCCGGTAATTTAGAAATAAGTGTTGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGTGCaa                                                                                              <  1:558226/145‑1 (MQ=255)                                              ttttttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATa                                                                                         >  2:585151/1‑150 (MQ=255)                                                       aagatATTAAGAAGAAAAAAGACAGAGAAAAAGAAAAAA‑TTCTCAATAAAGGGAGTAACATAGATATTAGGATTGCGAAAAATAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                                                                                <  1:667185/150‑1 (MQ=255)                                                       aaaaaaTTATGGAGAAAAATGAGAGGAAAAAAGAAAAAA‑TTCTAAAAAAATGCGTTAATTTAAAAATTAGTATTGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAg                                                                                  <  2:74978/145‑1 (MQ=255)                                                       aaaaaaTTATGGAAAAAAATGACAGGAAAAAAGAAGAAA‑TTCAAAAAAAAGGCGGTAACTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                                                                                <  1:169944/147‑1 (MQ=255)                                                       aaaaaaTTATGAAAAAAAATGAAAGGAAAAAAGAAAAAT‑TTCTAAAAAAATGGGTTAATTTAGATATTGGGTTTGGGGAAAAAAAAAGCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTa                                                                                <  1:499152/147‑1 (MQ=255)                                                          aatttATGAAAAAAAATGAAAGGAAAAAAGAAGAAA‑TTCCAAATAACGGCGGTAACTTAAAGATTTGGAGTGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAAc                                                                              <  2:644/146‑1 (MQ=255)                                                             ttaggaaaaaaaaTGACAGGAAAAAAGAAGAAA‑TTCAAAATAAATGCGGTAACTGAGAGATTAGGATGGAGAAAAATAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgt                                                                          <  1:615970/142‑1 (MQ=255)                                                             ttATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                         >  2:10259/1‑151 (MQ=255)                                                                 ggAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaa                                                                      >  2:418616/1‑150 (MQ=255)                                                                   aaaaaaaGGAGAGAAAAAAGGGAAAAA‑TTCTAAAAAAGGGCGTAAATTGAGAAATTGGGATAGGGAAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                     <  1:414128/147‑1 (MQ=255)                                                                      aaaaTGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg                                                                >  2:291983/1‑151 (MQ=255)                                                                        aaTGACAGGAAAAAAGGAGAAA‑TTCTAAATAAATGCGGTACCTTAGAGATTAGGTTTGCGGAAAATAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                              <  2:513039/151‑1 (MQ=255)                                                                         aggagaGGAAAAAGGGAAAAA‑TTCTAAATAAAGGCGTTACTTAAGAGATTAGGATGGCGGAAAAAAAAAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCaa                                                             <  2:679679/146‑1 (MQ=255)                                                                         aTGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                              >  1:508122/1‑150 (MQ=255)                                                                           gACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATc                                                           >  1:651764/1‑151 (MQ=255)                                                                            aCAGGAAAAAAGGAAAAA‑TTCTAAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAAt                                                            <  2:506236/149‑1 (MQ=255)                                                                                gaaaaaaGGAAAAA‑TTCTAAATAAATGCGTTAATTGAAATATTAGGATGGGGAAAAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTAt                                                        <  2:562773/147‑1 (MQ=255)                                                                                  aaaaaGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGt                                                     >  1:644942/1‑150 (MQ=255)                                                                                           aaa‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACtt                                           >  2:156373/1‑151 (MQ=255)                                                                                                tctcAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTccc                                       >  1:516633/1‑151 (MQ=255)                                                                                                 ctcAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCt                                      >  1:648544/1‑151 (MQ=255)                                                                                                   cAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTgg                                    >  2:194651/1‑151 (MQ=255)                                                                                                    aaTAAATGCGGTAATTTAGAGATTAGGATTGGGGAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTg                                     <  1:76555/149‑1 (MQ=255)                                                                                                     aaaaaTGCGGTAACTAAGAGATTAGGATTGGGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGtt                                  <  2:494365/149‑1 (MQ=255)                                                                                                                 aCTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTccc                      >  2:304858/1‑151 (MQ=255)                                                                                                                                  ggggAAAAAAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGc     <  2:168405/149‑1 (MQ=255)                                                                                                                                      agaATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGa  >  1:527336/1‑150 (MQ=255)                                                                                                                                       |                                                                                                                                                     ATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGA  >  NC_000913/5026‑5307

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑