Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,725	0	C	A	40.0%	72.8 / 16.4	41	intergenic (‑106/+35)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base C (22/2);  new base A (0/16);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 2.43e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAC  >  NC_000913/1435578‑1435874                                                                                                                                                    |                                                                                                                                                      tGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGc                                                                                                                                                       >  2:219932/1‑148 (MQ=255)  gAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAg                                                                                                                                                     <  2:394549/149‑1 (MQ=255)       ggAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGc                                                                                                                                              >  1:705032/1‑151 (MQ=255)                  tAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAAc                                                                                                                                    >  2:123368/1‑150 (MQ=255)                            attCGTTCTGTTAAAAAACCCTCCTTTTTTATTATCCGAAAAAAGTGAAACGCAAGATGACTTTTTTTGTGTAATGAGGGAGTTCATATTTTAAATTAAGATAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCagg                                                                                                                          <  2:626839/148‑1 (MQ=255)                                    ttttaaaaaacCCTCCTTTTTTAGTACCCCAAAAAAGTGTACCGCCAGAGAACATTTTTTGTGTATTGAGGGAGTTCACTTTTTTAATTTAGAACAAAGGAGAAAAAAAAAGAAGAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTa                                                                                                                  <  2:541280/143‑1 (MQ=255)                                         aTAAACCCTCTTTTTTTATTACCCGAAAAGAGTGAAACCCAAGATCCCTTTTTGTGTGAAATGACGGGTTACTTATTTTTAATTAAGACAAAAGGAGGAAAAAAAAGCAAAAAAACACCGCCATAACAGCGGGCAGGAGGATTTAGAACTg                                                                                                            <  2:686177/151‑1 (MQ=255)                                         aTAAAACCTCTTTTTTTATTATCCGAATAAAGTGAACCGCAAGATAACATTTTTTGTATAAGGACGAAGTCCAATTTTTAAATTGAGAAAAAAGGGGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                                             <  1:212201/150‑1 (MQ=255)                                                ctcctGGTTTAGAATCCGCATAAGGTGAAACGCCAGATGACACTTGTTGTGTAATTTCGGAGTTTACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAACCCCGCCGTAACAGCGGGCAGGAGGATTTAGAACTGa                                                                                                           >  1:172378/1‑145 (MQ=255)                                                    ttttttAGTACCCGAAAAAAGTGAAACGCCAGATGACTTTTTTGGTGAAATGAGGGATTTCACATTTTTAATTAAGAAAAAGGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCa                                                                                                    <  1:57622/146‑1 (MQ=255)                                                       tttAGTATCCGCAAAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGAGGGAGTTCACATTTTTAATTAAGATAAAAGGAGGAAAAAAAAG‑AAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTa                                                                                              <  2:478868/150‑1 (MQ=255)                                                       tttAGTACCCGAAAAAAGTGAAACGCAAGATGACTTTTTTTTTGAAAGGAGGGAGTTCAAATTTTTAATTTATAAAAAGGGAGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCt                                                                                               <  1:652101/150‑1 (MQ=255)                                                             aTCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCg                                                                                         >  1:157642/1‑150 (MQ=255)                                                               ccGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGa                                                                                        >  2:365813/1‑149 (MQ=255)                                                               ccGAATAAAGTGTAACGCCAGATGACTTTTTTTGTGTAAGGAGGGAGTTCACTTTTTTATTTTAAATAAAAGGAGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGAc                                                                                       <  2:362977/150‑1 (MQ=255)                                                                   aTAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAatat                                                                                  >  2:669858/1‑151 (MQ=255)                                                                   aTAAAGTGTAACGACAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCAGGAAGGAGGATTAAGAACTGATAAACCAGACCTAAAGCGACAatat                                                                                  >  1:499924/1‑151 (MQ=255)                                                                     aaaGTGAACCGCCAGACGACACTTTTGGTGTAAGGACGGATTACTCATTTTTAATTAAGAACAAAGGAGGAAAAAGAAGAAGAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatca                                                                                <  1:86154/151‑1 (MQ=255)                                                                          gaacctcaaaaTGACTTTTTTTGTGTAATGACGGATTTCACATTTTTATTTTAAAACAAAGGAGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCg                                                                             <  2:76344/139‑1 (MQ=255)                                                                                      gACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAtt                                                               >  2:3497/1‑151 (MQ=255)                                                                                           tttttGTGAAATGAGGGATTTCACATTTTTAATTTAGATCAAGGGAGAAAAAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTgg                                                             <  2:685892/148‑1 (MQ=255)                                                                                             tttGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCg                                                        >  1:102797/1‑151 (MQ=255)                                                                                                 tgtAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGt                                                       >  1:143299/1‑148 (MQ=255)                                                                                                  gtAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa                                                    >  2:138826/1‑150 (MQ=255)                                                                                                    aaTGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGc                                                 >  1:233456/1‑151 (MQ=255)                                                                                                        aCGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                                             >  1:250802/1‑151 (MQ=255)                                                                                                              ttCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTc                                       >  1:3143/1‑151 (MQ=255)                                                                                                                    tttttATTTTAAACAAAAGAAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCAt                                     <  2:462861/147‑1 (MQ=255)                                                                                                                    tttttATTTAAGAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCAt                                     <  1:134853/147‑1 (MQ=255)                                                                                                                    tttttAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                                  >  2:438305/1‑150 (MQ=255)                                                                                                                    ttttaAATTAAGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCa                                      <  2:705118/146‑1 (MQ=255)                                                                                                                     ttttAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                                >  2:637089/1‑151 (MQ=255)                                                                                                                      tttAATTAAGAGAAAAGGAGGAAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                                <  2:184530/150‑1 (MQ=255)                                                                                                                         aaTTAAGAACAAGGGAAAAAGAAAAAGAAAAAAAAACCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACa                               <  2:30290/148‑1 (MQ=255)                                                                                                                          aTTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt                           >  1:467151/1‑151 (MQ=255)                                                                                                                          aTTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGtt                           >  2:9856/1‑151 (MQ=255)                                                                                                                              aGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtt                       >  1:584132/1‑151 (MQ=255)                                                                                                                               gATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAttt                      >  2:470750/1‑151 (MQ=255)                                                                                                                                aacAAAGGAGGAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtttt                     <  2:308319/149‑1 (MQ=255)                                                                                                                                  cAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat                   >  1:394890/1‑151 (MQ=255)                                                                                                                                    aaGGAGGAAGAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGACTTTATAg                 <  2:662410/151‑1 (MQ=255)                                                                                                                                            agaaTAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCaa             >  2:534567/1‑147 (MQ=255)                                                                                                                                                    cAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAc  >  1:368800/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                      TGAATCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTTAGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAGTCAACGTAGGTGGAC  >  NC_000913/1435578‑1435874

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑