Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	5,159	0	G	A	62.2%	1.7 / 49.6	45	intergenic (+139/‑75)	thrC/yaaX	L‑threonine synthase/DUF2502 family putative periplasmic protein
Reads supporting (aligned to +/- strand):  ref base G (14/3);  new base A (0/28);  total (14/31)
Fisher's exact test for biased strand distribution p-value = 4.07e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.74e-08

CATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGG  >  NC_000913/5012‑5306                                                                                                                                                     |                                                                                                                                                     catcaGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGaa                                                                                                                                                    <  1:310951/150‑1 (MQ=255)      gTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATaaca                                                                                                                                               >  1:690067/1‑150 (MQ=255)        aaaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑cc                                                                                                                                           >  1:559618/1‑151 (MQ=255)        aaaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑cc                                                                                                                                           <  2:139331/151‑1 (MQ=255)         aaaTCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑ccg                                                                                                                                          <  1:19188/151‑1 (MQ=255)             cTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGt                                                                                                                                      >  1:499782/1‑151 (MQ=255)                ttCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTtct                                                                                                                                   >  2:330821/1‑151 (MQ=255)                   aTTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGTTTTTTTATGAAGAAATTATGAAAAAAAATGACAGGAAAAAAGAAAAAA‑TTCTCAAAAAATGCGATAACTTAGAGATTAGGTTGGCGGAAAATAACAA‑CCGCCGTtctc                                                                                                                                  <  1:601600/149‑1 (MQ=255)                           aaacAGGCCGGTTTTTTTTTTAGGAAGCCGGGTTTTTTTATGAAAAATTTGGGGAAAAAAATGACAGGAAAAAGGGAAAAA‑TTCTCAATAAATGCGTTAACTTAGATATTGGGATGGGGAAAAATAAAAA‑CCGCCGTTCTCATCGAGt                                                                                                                           <  1:156191/145‑1 (MQ=255)                           aaTCAGGCGGTTTTTGTTTTTATGCAGCCCGGTTTTTTTATGAAAAAATTAGGGAAAAAAATGAAAGGAAAAAAGGAAAAA‑TTCTAAATAAATGCGTTAACTTAGAGATTAGGATTGGGAAAAAAAACAA‑CCGCCGTTCTCATCg                                                                                                                              <  1:342266/145‑1 (MQ=255)                           aaTCAGGCGGGGTTTGTTTTTATGCACCCCGGTTTTTTTATAAAAAATTTAGGGAAAAAAATGACAGGAAAAAAGGAAAAA‑TTCTCAATAAAGGCGTTAACTTAGAAATTAGGATTGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTaa                                                                                                                         <  1:447120/150‑1 (MQ=255)                                ggCCGGGTTTGTTTTTATGCAGCCCGGTTTTTTTAAAAAAAAATTAGGAAAAAAAATGACAGGAAAAAAGGAGAAA‑TTCTCAATAAAGGCGGTAACGTAGAAATTGGGATTGCGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTcc                                                                                                                    <  1:525580/150‑1 (MQ=255)                                   cGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGat                                                                                                                >  1:408966/1‑151 (MQ=255)                                    ggttttGTTTTAAGGCAGCCCGTTTTTTTTAAGAAAAAATTATGGAAAAAAAGGAAAGGAAAAAAGAAAAAT‑TTCTCAATAAAGGCGGAAACTTGAAGATTAGGATGGGGAAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGa                                                                                                                 <  1:618043/146‑1 (MQ=255)                                    ggttttGCTTTTAGGCAGCCCGGTTTTTTTATAAAAAAATTAGGGAAAAAAAGGACAGGAAAAAAGAAAAAA‑TTCTAAAAAAAGGCGGTAATTTAGAGATTAGGATGGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGata                                                                                                               <  2:91412/148‑1 (MQ=255)                                    gggTTTTTTTTTATGCACCCCGGTTTTTTTATAAAAAAATTAGGGAAAAAAAGGACAGGAAAAAAGGAAAAA‑TTCTAAAAAAAGGGGGTAACTTAGAGATTAGGATGGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGata                                                                                                               <  2:617435/151‑1 (MQ=255)                                     ggTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                                              >  2:163052/1‑151 (MQ=255)                                       tttGCTTTTAGGCAGCCCGTTTTTTTTATAAAGAATTTATGGAAAAAAAGGAAAGGAAAAAAGGAGAAA‑TTCTAAATAAATGCGGTAATTTAGAGATTAGGATGGCGGAAAATAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGatat                                                                                                              <  2:680593/149‑1 (MQ=255)                                            ttttATGCACCCCGGTTTTTTTATAAAAAAATTATGGAAAAAAATGACAGGAAAAAAGGAGAAA‑TTCTAAAAAAAGGCGGAAACTTAGAGATTAGGATTGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGAccc                                                                                                        <  2:490669/150‑1 (MQ=255)                                            tttaATGCAGCCCGGCTTTTTTATAAAAAAATTAGGGAAAAAAAGGACAGGAAAAAAGAAAAAA‑TTCTAAAAAAGTGCGTTAATTTAGATATAAGGATTGCGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGAcc                                                                                                         <  1:252478/149‑1 (MQ=255)                                                      cccgttttttttAAGAAAAAATTATGAAAAAAAATAAAAGGAAAAAAGGAAAAT‑TTCACAAAAAATGCGTTAACTGAGAGATTAGGATTGCGGAAAAAAACAC‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGc                                                                                               <  1:412884/143‑1 (MQ=255)                                                      cccGGCTTTTTTATGAAAAAATTATGGAAAAAAATGACAGGAAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGTTTGGGGAAAATAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACgg                                                                                                 <  1:582991/147‑1 (MQ=255)                                                       ccGGATTTTATAAAAAAAAATAAGGAAAAAAAAGGAAAGGAAAAAGGGAAAAA‑TTCACAAAAATCGCGGTAATTTAAAAATGGGGAGTGGGGAAAACAACAG‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATa                                                                                                     <  1:486472/142‑1 (MQ=255)                                                             tttttATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaa                                                                                       >  1:590645/1‑150 (MQ=255)                                                              ttttATAAAAAAATTAGGGAAAAAAATGAGAGGAAAAAAGGAAAAA‑TTCTCAAAAAATGCGGTAACTTAGAGTTTAGGTTTGGGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATaaa                                                                                      <  2:105083/150‑1 (MQ=255)                                                                     aaaaaaTTAGGAAAAAAAATGAGA‑GGAAAAAGGAAAAATTTCTAAAAAATTGCGATAATTGAGAATTAAGGATTGCAGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGa                                                                                  <  1:193818/144‑1 (MQ=255)                                                                     aaaaaaTGAGGGAAAAAAAGGGGAGGAAAAAGGGAAAAA‑TTCCAAATAATGGCTGTATTTGAGA‑AATAGGTTTTGGGAAAAAAAAAATCCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAgg                                                                                   <  1:186186/143‑1 (MQ=255)                                                                            tATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCtgtg                                                                        >  1:34993/1‑150 (MQ=255)                                                                                 aaaaaaaTGACAGGAAAAAAGGAAAAT‑TTCTAAAAAAAGGCGTTATTTTAGATTTTAGGATGGGGAAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGa                                                                       <  1:709348/144‑1 (MQ=255)                                                                                 aaaaaaaTGAAAGGAAAAAAGGAAAAA‑TTCTAAAAAAAGGCGGTAACTAAGAGATTAGGATGGCGGAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGaaaa                                                                    <  1:584135/147‑1 (MQ=255)                                                                                    aaaaTGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATg                                                               >  2:600061/1‑151 (MQ=255)                                                                                      aaTGAAAGGAAAAAAGGAAAAA‑TTCTCAAAAAATGCGTTAACTTAGAGATTAGGATTGCGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCa                                                             <  1:296362/151‑1 (MQ=255)                                                                                         gaagggaaaaaaGGAAAAA‑TTCTAAATAAATGCGTTAATTGAAAGATAAGTTGGGCGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCaa                                                            <  2:559766/142‑1 (MQ=255)                                                                                          aCAGGGAAAAAGGAAAAA‑TTCAAAAAAAATGCGAAAATTTAAAGATTAGGGTTGGGAAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCaa                                                            <  1:415981/148‑1 (MQ=255)                                                                                          aCAGGAAAAAAGGAAAAA‑TTCAAAATAAATGCGGTAATTAAGAAATTAGGATGGCGAAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCt                                                         <  1:659410/151‑1 (MQ=255)                                                                                                  aaaGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                                 >  1:706418/1‑151 (MQ=255)                                                                                                  aaaGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACt                                                 >  2:362739/1‑151 (MQ=255)                                                                                                                tcAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTg                                    >  1:158004/1‑151 (MQ=255)                                                                                                                  aaaaaaGGCGGAAACTTAGAGATTAGGATTGGGGAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTcc                                       <  2:668144/143‑1 (MQ=255)                                                                                                                     aaaTGCTTTAATTAAAAGTTTAGTATGGCGAAAAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCt                               <  1:707201/151‑1 (MQ=255)                                                                                                                     aaaTGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCt                               >  2:221721/1‑151 (MQ=255)                                                                                                                              aaCTGAGAGATGGGGATGGCGGAAAAAAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCt                        <  1:298519/149‑1 (MQ=255)                                                                                                                                   agaatttAGGATTGCGGAAAAAAAAAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTccc                     <  1:425459/142‑1 (MQ=255)                                                                                                                                    gagaTTAGGTTTGGGGAAAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCAt                   <  2:392656/148‑1 (MQ=255)                                                                                                                                                  ggAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCgg  >  2:421471/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                     CATCAGTAAAATCTATTCATTATCTCAATCAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAAAGGAGAAA‑TTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAA‑CCGCCGTTCTCATCGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATCTATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGG  >  NC_000913/5012‑5306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑