Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,435,721	0	T	A	43.4%	76.5 / 27.7	53	intergenic (‑102/+39)	uspF/ompN	stress‑induced protein, ATP‑binding protein/outer membrane pore protein N, non‑specific
Reads supporting (aligned to +/- strand):  ref base T (25/5);  new base A (0/23);  total (25/28)
Fisher's exact test for biased strand distribution p-value = 2.61e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAG  >  NC_000913/1435582‑1435859                                                                                                                                             |                                                                                                                                           tCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGaaaa                                                                                                                                  >  2:102845/1‑150 (MQ=255)    gAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGcc                                                                                                                              >  1:596077/1‑151 (MQ=255)     aaaTATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGccc                                                                                                                             <  1:140150/151‑1 (MQ=255)          tCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCa                                                                                                                         <  1:370190/150‑1 (MQ=255)           cGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCAt                                                                                                                        >  1:748499/1‑150 (MQ=255)               aGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAAc                                                                                                                     >  1:743805/1‑149 (MQ=255)                   aCAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCggg                                                                                                               >  1:725327/1‑151 (MQ=255)                             ttttGTTAATAAACCCTCTTGTTTTAGTATCCACAAAAAGTGTAACGCCAGATAACATTTTTTGTAAAAGGGCGGACTCCACTTTTTTATTTT‑AGACCAAAGAAGAAAAAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAggagga                                                                                                       <  1:244049/146‑1 (MQ=255)                                  ttaaaaaacCCTCCTTTTTTAGTATCCAAAAAAAGTGAACCGCAAGATGACTTTTTTTGTGAAATGAGGGAGTTCACATTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                    <  2:912773/142‑1 (MQ=255)                                  ttaaaaaacCCTCCTTTTTTAGTACCCGAAAAAAGTGAAACGCAAGATGCCTTTTTTTGTTTAAGGAGGGATTTCACTTTTTTATTTA‑AGAAAAAAGAAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGAttt                                                                                                    <  1:771857/142‑1 (MQ=255)                                    cATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                              >  2:487313/1‑151 (MQ=255)                                    cATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACt                                                                                              >  1:360861/1‑151 (MQ=255)                                         aaCCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATa                                                                                          >  1:170616/1‑150 (MQ=255)                                                tGTTTTAGTACCCGAATAAAGTGAAACGCAAAATGACTTTTTTTGTGAAAGGACGGAGTTCACTTTTTAAATTA‑AAAAAAAAGGGGAAAGAATAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAg                                                                                    <  1:875014/149‑1 (MQ=255)                                                 gTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGAcc                                                                                 >  2:499107/1‑151 (MQ=255)                                                  ttttAGTCTCCGAATAAAGTGTAACGCCAGATAACTTTTTTTGTGTAATGACGGAGTTCCTATTTTAAATTT‑AGATAAAAGGAGGAAAAATAAGCAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAAcc                                                                                      <  2:398020/145‑1 (MQ=255)                                                  ttttAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCt                                                                                >  1:622220/1‑151 (MQ=255)                                                      aGTACCCGAAAAAAGTGAACCCCAAGATGACATTTTTGGTGAAAGGAGGGATTTCACTTTTTTAATTA‑AGATAAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTaa                                                                              <  1:688502/149‑1 (MQ=255)                                                         aTCCGAAAAAAGTGTAACGCAAGATGACATTTTTGTTGAAAGGACGAAGTTCACATTTTTAATTT‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGc                                                                           <  1:884079/149‑1 (MQ=255)                                                               aTAAAGTGTAACGCCAGATGACTCTTTTTGTGTAATGAGGGAGTTCATTTTTTTAATTA‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAat                                                                     <  1:687645/149‑1 (MQ=255)                                                                tAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatc                                                                  >  2:683340/1‑151 (MQ=255)                                                                   aGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatcatc                                                               >  1:46528/1‑151 (MQ=255)                                                                   aGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATatcatc                                                               >  2:13614/1‑151 (MQ=255)                                                                        aaCGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                            >  1:66943/1‑149 (MQ=255)                                                                        aaCGCAAGATGACTTTTTTTGTGTAAGGAGGGAGTTCATTTTTTTATTTA‑AAAAAAAGGGAGAAAAAAAAAAAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTa                                                           <  1:158507/150‑1 (MQ=255)                                                                        aaCCCCAGATGACTTTTTTTGTGTAAGGACGGATTTCACTTTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGt                                                            <  2:163160/149‑1 (MQ=255)                                                                           gCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTag                                                          >  2:884536/1‑148 (MQ=255)                                                                                aggACTCTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGc                                                    <  2:505698/147‑1 (MQ=255)                                                                                 tgattttttttGTGAAATGACGGA‑CTCCGATTTTTAATTTAAGAAAAAGGGGAAAAAAAAAAACAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGAt                                                      <  1:753629/140‑1 (MQ=255)                                                                                 tGACATTTTTTGTGAAATGAGGGATTTCATTTTTTAAATTA‑AAAACAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCa                                                  <  1:518458/150‑1 (MQ=255)                                                                                 tGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCAt                                                 >  2:850313/1‑151 (MQ=255)                                                                                     acTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGc                                             >  2:169405/1‑151 (MQ=255)                                                                                        ttttGTGAAATGAGGGAGTTCACTTTTTTAATTT‑AGAAAAAAGGAGGAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAg                                           <  1:150347/150‑1 (MQ=255)                                                                                         tttGTGAAATGAGGGATTTCAAATTTTTAATTA‑AAATAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                          <  1:884511/150‑1 (MQ=255)                                                                                         tttGTGAAATGACGGATTTCACATTTTTAATTT‑AGAAAAAAGGAGAAAAAAAAAAAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGc                                          <  1:387237/150‑1 (MQ=255)                                                                                           tgtgTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGt                                        >  2:342218/1‑150 (MQ=255)                                                                                                aaggggggATTTCAATTTTTTAATTA‑AAAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGa                                     <  1:556063/142‑1 (MQ=255)                                                                                                aaTGCCGGATTTCATTTTTTTAATTA‑AGAAAAAAGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAg                                   <  1:333594/150‑1 (MQ=255)                                                                                                    aCGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTc                              >  2:482858/1‑151 (MQ=255)                                                                                                      ggAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCAt                            >  1:517835/1‑151 (MQ=255)                                                                                                        aGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGACATCt                          >  2:97673/1‑151 (MQ=255)                                                                                                         gTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCtt                         >  1:965281/1‑151 (MQ=255)                                                                                                           tCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTc                        >  2:353940/1‑150 (MQ=255)                                                                                                             ataTTTTAAATTT‑AGATAAAGGGGGAAAAAAAAACCAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCa                       <  1:683490/147‑1 (MQ=255)                                                                                                                tttttAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCa                   >  2:807453/1‑150 (MQ=255)                                                                                                                tttttAATTA‑AAAAAAAAGGAGAAAAAAAAAGAAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATcc                    <  2:41835/149‑1 (MQ=255)                                                                                                                   ttaatta‑aGATAAAGGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACa                <  1:757493/150‑1 (MQ=255)                                                                                                                   ttaatta‑aGAACAAAGGAGGAATAAAAGGAAAAAAAGGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAAc                 <  1:891073/149‑1 (MQ=255)                                                                                                                     aaTTA‑AGAAAAAGGGAGAAAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAgg              <  1:177942/150‑1 (MQ=255)                                                                                                                           agacaaagggagaaAAAAAAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGAtt        <  1:122073/143‑1 (MQ=255)                                                                                                                               cAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTtat    >  2:416788/1‑151 (MQ=255)                                                                                                                                 aaGGAGAAAGAATAAGAAAAAAAACCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAg  <  1:10062/151‑1 (MQ=255)                                                                                                                                 aaGGAGAAAAAAAAAGCAAAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAg  <  1:532507/151‑1 (MQ=255)                                                                                                                                             |                                                                                                                                           TCGGAAATATCGATAGGGACAAGAATCGTTCTGTTCATAAAACCTCCTGTTTTAGTATCCGCATAAAGTGTAACGCCAGATGACACTTTTTGTGTAATGACGGAGTTCACATTTTTAATTT‑AGATCAAAGGAGGAAGAATAAGCAGAAAAAGCCCGCCATAACAGCGGGCAGGAGGATTTAGAACTGATAAACCAGACCTAAAGCGACAATATCATCGGTAGAGATGCCATTGGCAGCGTAGAAGCTGTCATCTTCATCCAACAGGTTGATTTTATAG  >  NC_000913/1435582‑1435859

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑