Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,864,099	0	C	A	45.8%	61.2 / 22.4	48	R67R (CGC→CGA)	yidP	UTRA domain‑containing GntR family putative transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (20/6);  new base A (0/22);  total (20/28)
Fisher's exact test for biased strand distribution p-value = 1.62e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

AGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCA  >  NC_000913/3863949‑3864244                                                                                                                                                        |                                                                                                                                                  aGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTgcgc                                                                                                                                                   >  2:575044/1‑151 (MQ=255)      tCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCaa                                                                                                                                                 >  1:724252/1‑148 (MQ=255)              aaCAGCCTTCTTCCCGGTGAAAAAAGGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGc                                                                                                                                      >  1:103304/1‑151 (MQ=255)                        ttcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGc                                                                                                                            >  1:193569/1‑151 (MQ=255)                         tcCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAAcc                                                                                                                              <  2:342921/148‑1 (MQ=255)                                  aaaaaaGCTGGCGGAAGAGTTGGGGGTGCCGGGGATGCCCATCCGTAAAGCC‑ATTGCCCTGCTGGTGGGGGGGGGGCTGGTGGTCCGCCCCCACGGTAGTGGCATTTCCCGGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGAcc                                                                                                                  <  2:864597/151‑1 (MQ=255)                                   aaaaaGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCg                                                                                                                 >  1:607636/1‑151 (MQ=255)                                      aacgtggagaaaGAGTTTGCGGTCTCGCGTGTGGCCATCCGTAATGCC‑GTTGCCCTGCTGGTAGGGTGGGGGCTGGTGGTCCCCCGCCACGGTAGTGGCACTTACCTGTTGCGCAAAATTGCTCTGCACCAAACCGCCAGTCTGACCGGGc                                                                                                              <  1:170930/141‑1 (MQ=255)                                             cGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCtggtgg                                                                                                        >  1:36261/1‑150 (MQ=255)                                              gaaaGAGTTTGCGGTCTCGGGGATACCCACCGGAAAAGCC‑TTTGCCCGGCTGGGGGGGGGGGGGCTGGTGGTCCGCCGCCAGGGTGGTGGCACTTCCCGGGTGCGAAAAGATGTACTGAATCAAACCGCCAGTCTGACCGGGCTGGTGGAg                                                                                                      <  2:906657/149‑1 (MQ=255)                                                    gTTTGGGGTCTGGCGTATGACCGT‑CGTAAAACCGATTGCCTGGTTGTTAGGGGGGGGGTTGGGGGTCCCCCCCCCCGGTAGTGGCACTTTCTTGTTGTGAAAAGATGTACGGCTTCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGtt                                                                                                 <  1:179898/150‑1 (MQ=255)                                                       tGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTaaa                                                                                              >  1:920197/1‑150 (MQ=255)                                                        gCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAAc                                                                                            >  1:191704/1‑151 (MQ=255)                                                              tcggggagacccACCCGAAAACCA‑ATTGTCCTTCGGATGGCGGGGGGGCTGGTGGCCCGCCCCCACGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACCGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAg                                                                                       <  1:979450/140‑1 (MQ=255)                                                              tCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAgg                                                                                      >  1:801685/1‑151 (MQ=255)                                                                gcgGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAggg                                                                                     >  2:799618/1‑150 (MQ=255)                                                                gcgGATGACCACCCGTAAAGCC‑ATGGACCGGCGGGAGGCGGGGGGGCTGGTGGTCCGCCGCCACGGTGGTGGCCCTTCCCTGGTGCGAAAAGTTGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGa                                                                                    <  1:555470/151‑1 (MQ=255)                                                                  ggATGCCCATCCGAAAGGCC‑ATTGCCCTGCTGGTGGGGTGGGGGCTGGTGGTCCGCCGCCACGGTGGTGGCACTTACCTGGTGCGAAAAGATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGaa                                                                                   <  1:190159/150‑1 (MQ=255)                                                                          aTCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGATCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACCGCATCAAACAGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACg                                                                              >  2:390915/1‑147 (MQ=255)                                                                               tAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagc                                                                     >  1:273840/1‑151 (MQ=255)                                                                                aaaGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcc                                                                    >  2:931333/1‑151 (MQ=255)                                                                                aaaGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcc                                                                    >  2:58932/1‑151 (MQ=255)                                                                                aaaGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagcc                                                                    >  2:402361/1‑151 (MQ=255)                                                                                     cctttGCCCTGCTGGTGGCGTGGGGGCGGGTGGTCCGCCGCCACGGTAGTGGCCCTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCAccagccag                                                                  <  1:485905/146‑1 (MQ=255)                                                                                        tggcccTGCTGGGAGTGGGGGGGGTGGTGGCCCGCCCCCAGGGTAGTGGCACTTACCGGGGGCGAAAAGATTTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGt                                                                <  2:48994/144‑1 (MQ=255)                                                                                                 tgGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTg                                                     >  1:859813/1‑150 (MQ=255)                                                                                                  ggTGGCGGGGGGGCTGGTGGTCCGCCGCCAGGGTAGTGGCACTTACCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTg                                                     <  1:251123/149‑1 (MQ=255)                                                                                                  ggTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGa                                                    >  2:798766/1‑150 (MQ=255)                                                                                                    tcgCGGGGGGGCTGGTGGTCCCCCGCCACGTTAGTGGCACTACCCTGGTGCAAAAAGATGTCCTGAATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGaa                                                   <  1:533032/147‑1 (MQ=255)                                                                                                      gCGTGGGGGCTGGTGGCCCGCCGCCACGGTAGTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAAt                                                 <  1:983603/149‑1 (MQ=255)                                                                                                      gCGGGGGGCCTGGGGGCCCCCCCCCACGGGGGTGGCACTTCCCTGGTGCGAAAAGTTGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCa                                               <  2:933347/151‑1 (MQ=255)                                                                                                        gTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATg                                             >  1:745979/1‑151 (MQ=255)                                                                                                            gggCTGGTGGTCCGCCGCCACGGTGGTGGCCCTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTg                                         <  2:364398/151‑1 (MQ=255)                                                                                                                 ggtggtCCGCCGCCAGGGTAGTGGCACTTCCCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGcc                                     <  1:959846/150‑1 (MQ=255)                                                                                                                 ggtggtCCGCCGCCACGGTGGTGGCACTTCCGTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCt                                    <  2:22846/151‑1 (MQ=255)                                                                                                                    ggtCCCCCGCCCGGGTGGTGGCTCTTCCCGGGTGCGAAAAGTTTTTCGGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCg                                 <  2:50907/151‑1 (MQ=255)                                                                                                                          ccgccgCGGTAGGGGCCCTTACCGGGTGCGAAAAGATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGc                               <  1:957215/147‑1 (MQ=255)                                                                                                                          ccgccCGGGTAGTGGCTCTTACCGGGTGCGAAAGGGTGCACTGCAGAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCAtt                           <  1:197920/151‑1 (MQ=255)                                                                                                                           cgccAGGGTAGGGGCACTTCCCGGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTg                          <  1:255114/151‑1 (MQ=255)                                                                                                                            gccACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgc                         >  2:696881/1‑151 (MQ=255)                                                                                                                             ccACGGTGGGGGCACTTCCCTGGTGCGAAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTg                          <  1:725718/149‑1 (MQ=255)                                                                                                                                  gTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTgccagcc                    >  2:839178/1‑150 (MQ=255)                                                                                                                                     gTGGCACTTCCCTGGTGCGAAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGtt                <  1:261324/151‑1 (MQ=255)                                                                                                                                             tcccTGGTGCGCAAGGTTGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAt          <  2:966849/147‑1 (MQ=255)                                                                                                                                               ccTGGTGCGCAAAGATGTACTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGa           <  2:715198/146‑1 (MQ=255)                                                                                                                                               ccTGGTGCGAAAAGATGTCCTGCATAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGAtt         <  2:315817/148‑1 (MQ=255)                                                                                                                                                 tGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAAt    >  2:386044/1‑151 (MQ=255)                                                                                                                                                  ggTCCGCAAAGATGTACGCCGTCAAGCCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCaaa     <  1:152795/149‑1 (MQ=255)                                                                                                                                                   gTGCGAAAAGAGGTACTGCACAAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCa  <  2:697652/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                  AGATTTCACGCTAAACAGCCTTCTTCCCGGTGAAAAAAAGCTGGCGGAAGAGTTTGCGGTATCGCGGATGACCATCCGTAAAGCC‑ATTGACCTGCTGGTAGCGTGGGGGCTGGTGGTCCGCCGCCACGGTAGTGGCACTTACCTGGTGCGCAAAGATGTACTGCATCAAACCGCCAGTCTGACCGGGCTGGTGGAGGTGTTAAAACGGCAGGGAAAAACGGTCACCAGCCAGGTGCTGATTTTTGAAATCATGCCTGCGCCTCCGGCCATTGCCAGCCAGTTACGGATTCAAATCA  >  NC_000913/3863949‑3864244

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑