Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,864,089	0	A	C	41.2%	81.4 / 10.9	51	Y64S (TAC→TCC)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (23/7);  new base C (0/21);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.08e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACTCCGCAGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATT  >  NC_000913/3863940‑3864237                                                                                                                                                      |                                                                                                                                                     tAACTCCGCAGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTa                                                                                                                                                      <  1:561681/150‑1 (MQ=255) tAACTCCGCAGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTa                                                                                                                                                      <  2:867955/150‑1 (MQ=255)     tCCGCAGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTgg                                                                                                                                                 >  1:889224/1‑151 (MQ=255)          aGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTgcgc                                                                                                                                            >  1:181199/1‑151 (MQ=255)              ttCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCaaa                                                                                                                                         <  2:270301/150‑1 (MQ=255)                 aCGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATg                                                                                                                                     >  1:625560/1‑151 (MQ=255)                         cAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCAt                                                                                                                             <  2:8313/151‑1 (MQ=255)                                 ttcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGc                                                                                                                     >  1:414084/1‑151 (MQ=255)                                  tcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGGTGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGcc                                                                                                                    >  1:33026/1‑151 (MQ=255)                                    ccGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGcc                                                                                                                    >  1:392827/1‑149 (MQ=255)                                      ggTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTc                                                                                                                >  1:431453/1‑151 (MQ=255)                                               aaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGc                                                                                                       >  1:599483/1‑151 (MQ=255)                                                 gCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtg                                                                                                     >  1:186813/1‑151 (MQ=255)                                                    ggCGGAAGAGTTTGCGGTATCGGGGATGACAACCCGAAAAGCCATTGCCCTGCTGGTGGGGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGAAAAGATGTACTGAATAAAACCGCCAGTCTGACCGGGCtggtg                                                                                                  <  1:991253/151‑1 (MQ=255)                                                                   ggTATCGCGGATGACCATCCGTAAAGCCATTGCCCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCATTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACgg                                                                                   <  2:600359/151‑1 (MQ=255)                                                                   ggTATCGCGGAGGACCATCCGAAAAGCCATTGCCCTGCTGGTAGGGGGGGGGCGGGTGGTCCGCCGCCACGGTAGGGGCACTTCCCTGGGGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTaaaa                                                                                      <  2:394098/148‑1 (MQ=255)                                                                   ggTAGCGGGGAGGACCATCCGAAAGGCCATTGACCTGCTGGTGGCGTGGGGGGTGGTGGTCCGCCGCCACGGTGGGGGCATTTCCCTGGTGCACAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTaaaa                                                                                      <  2:746705/148‑1 (MQ=255)                                                                     tagcgcggaaagccatccatAAATCCAGTGACGATATGATAGTTTGGGGGCTGGTGGCCCGCGGCCTGGGTGTTAACATTTCCGTGGTGCGGAAGATTGTACTCAATGAATCCGACAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                  <  2:692078/138‑1 (MQ=255)                                                                      aTCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                  >  2:393481/1‑149 (MQ=255)                                                                      aTCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGc                                                                                  >  2:726084/1‑149 (MQ=255)                                                                        cgcgGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAggg                                                                              >  2:514262/1‑151 (MQ=255)                                                                         gcgGATGACCATCCGAAAAGCCTTGGCCCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCCCTTCCCGGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAgg                                                                               <  2:500876/149‑1 (MQ=255)                                                                             aggACCACCCGAAAACCAATTGACCGGGTGGTGGGGGGGGGGTTGGTGGTCCCCCGCCAGGGTAGTGGCCCTTCCCTGGTCGGAAAGGATTTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaaa                                                                         <  1:349781/149‑1 (MQ=255)                                                                             aTGCCCATCCGTAAAGCCATTGTCCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCCCTTCCCTGGTGCGCAAGGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaaa                                                                         <  2:737324/151‑1 (MQ=255)                                                                              ggACCATCCGAAAAGCCTTTGACCTGCTGGTAGGGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaaaa                                                                          <  1:328508/148‑1 (MQ=255)                                                                               gACCGTCCGTAACGCATTGGCCCTGCGGGTGGCGGGGGGGGTGGTGGTCCGCCGCCAGGGTGGGGGCATTTCCCTGGGGGGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACg                                                                       <  1:50606/151‑1 (MQ=255)                                                                                 ccACCCGTAAAGCCATTGCCCTGCTGGTAGCGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGt                                                                     <  2:431460/151‑1 (MQ=255)                                                                                   aTCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCGGGTGCGAAAAGATTTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGt                                                                     <  1:249435/149‑1 (MQ=255)                                                                                         aaaGCCATTGCCCTGCTGGTGGGGGGGGGGCTGGTGGTCCGCCGCCACGGTGGTGGCACTTCCCGGGGGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAcca                                                                <  1:843968/148‑1 (MQ=255)                                                                                             ccATTGCCCGGCTGGTAGGGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGt                                                         <  1:238575/151‑1 (MQ=255)                                                                                              cATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTg                                                        >  1:573587/1‑151 (MQ=255)                                                                                                  gACCTGCGGGTAGGGTGGGGGCTGGGGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGa                                                    <  1:1021774/151‑1 (MQ=255)                                                                                                    ccTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTg                                                     <  2:282179/148‑1 (MQ=255)                                                                                                       gctgGTGGGGGGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCGGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGAttt                                                 <  1:801868/149‑1 (MQ=255)                                                                                                        ctgGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTg                                              >  2:859028/1‑151 (MQ=255)                                                                                                                gTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATg                                      <  2:152572/151‑1 (MQ=255)                                                                                                                gTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATg                                      >  1:957218/1‑151 (MQ=255)                                                                                                                gTGGGGGCTGGTGGTCCCCCGCCACGGTAGTGGCACTTACCTGCTGCGCAAAGATGCACTGCATCAAACCGCCAGTCGCAGCGGGATGGTGGAGGAGATAAAATGGCGGGGATAAACGGTCACGAGCAAGGCGCGCAGTTTTGTAATCAt                                       >  1:329223/1‑150 (MQ=255)                                                                                                                  gggggCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGc                                     <  2:852707/150‑1 (MQ=255)                                                                                                                     ggCTGGTGGTCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTgc                                 <  2:495611/151‑1 (MQ=255)                                                                                                                      gCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTgcg                                >  2:434968/1‑151 (MQ=255)                                                                                                                         ggtggcCCGCCGCCACGGTAGGGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTgcgc                               <  1:877889/149‑1 (MQ=255)                                                                                                                            gtccccccgccACGGTGGGGGCACTTCCCTGGTGCGAAAAATTGTACGGAAACAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTc                            <  1:454812/143‑1 (MQ=255)                                                                                                                            ggtCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTcc                           <  2:263961/150‑1 (MQ=255)                                                                                                                              tCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGc                        >  2:360704/1‑151 (MQ=255)                                                                                                                                     ccccgttAGGGGCACTTACCGGGTGCGAAAGGATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgcc                 <  2:977851/145‑1 (MQ=255)                                                                                                                                        cGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagc              >  1:44268/1‑151 (MQ=255)                                                                                                                                             gTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGtt         >  2:456416/1‑151 (MQ=255)                                                                                                                                             gTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGtt         >  2:206399/1‑151 (MQ=255)                                                                                                                                               ggCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTa        <  2:414090/150‑1 (MQ=255)                                                                                                                                               ggCACTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGtt         <  2:950034/149‑1 (MQ=255)                                                                                                                                                 cACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACgg     >  1:136181/1‑151 (MQ=255)                                                                                                                                                     tACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAtt  >  1:3921/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                     TAACTCCGCAGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCCATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATT  >  NC_000913/3863940‑3864237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑