Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	23.3%	81.7 / 15.9	43	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/32);  new base T (10/0);  total (11/32)
Fisher's exact test for biased strand distribution p-value = 5.74e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01
Rejected as consensus: Frequency below/above cutoff threshold.

AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206298‑3206566                                                                                                                                            |                                                                                                                                      aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑Ca                                                                                                                                    <  2:1675510/140‑1 (MQ=255)        tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTT‑CAaaa‑aaaa                                                                                                                            >  2:57630/1‑139 (MQ=255)           cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACTTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACa                                                                                                                         <  1:622605/140‑1 (MQ=255)               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGA‑G‑AATTTTTT‑TTAAc‑aaaaacaaaaa                                                                                                                     >  2:249803/1‑140 (MQ=255)                ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAAc                                                                                                                    <  2:1620783/140‑1 (MQ=255)                    ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTT‑CCGAC‑Aaaaaaaaaaaaagga                                                                                                                >  1:445602/1‑135 (MQ=255)                     tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAg                                                                                                               <  2:1772879/140‑1 (MQ=255)                     tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAg                                                                                                               <  2:188117/140‑1 (MQ=255)                     tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAg                                                                                                               <  2:1087531/140‑1 (MQ=255)                     tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAg                                                                                                               <  1:418129/140‑1 (MQ=255)                       tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTT‑TCGAC‑AAAAAAAAAAAATAGAGtt                                                                                                             >  2:1755470/1‑140 (MQ=255)                         gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTC‑CA‑AC‑AAAAAAAAAAAAAGGAGtttc                                                                                                           >  2:758595/1‑138 (MQ=255)                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGcc                                                                                                          <  2:461321/140‑1 (MQ=255)                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCatga                                                                                                      <  2:326093/140‑1 (MQ=255)                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGC‑G‑TAATTTTC‑CAGAA‑AAATAAAAAAAATTGAGGTgggatgt                                                                                                      >  2:1518329/1‑134 (MQ=255)                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAg                                                                                                  <  2:197494/140‑1 (MQ=255)                                     ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATTAGCGa                                                                                               <  2:1357141/140‑1 (MQ=255)                                     ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                               <  1:971419/140‑1 (MQ=255)                                            tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                        <  1:453160/140‑1 (MQ=255)                                              tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTT‑CAGAA‑AAAAAAAAAAAAAGGAGGTGGCATGATGGGCGGAAGaaaaaa                                                                                      >  2:916241/1‑140 (MQ=255)                                              tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaataa                                                                                      <  2:618085/140‑1 (MQ=255)                                                gacaggATTCACAAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGc                                                                                    <  1:466146/135‑1 (MQ=255)                                                      aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  1:1611366/140‑1 (MQ=255)                                                      aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  1:380649/140‑1 (MQ=255)                                                       ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                             <  1:1518329/140‑1 (MQ=255)                                                        tCATGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCa                                                                            <  1:1750032/140‑1 (MQ=255)                                                             aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:57630/140‑1 (MQ=255)                                                             aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:340885/140‑1 (MQ=255)                                                                tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑TAATTTTT‑CAGAA‑AAAAAAAAAAAATGGAGTTTTCATGAAGAGGGGAAAGAAAAAACTACAGACAGTgcggga                                                                    >  2:466146/1‑135 (MQ=255)                                                                tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑GAATTTTT‑CAGAC‑AAAAAAAAAAAAATGAGGTGCCCTGATGAGGGAAAAAAAAAAAAAAAAAGCAGTGAaaaa                                                                    >  2:380649/1‑140 (MQ=255)                                                                  ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTT‑CAGAC‑AAAAAAAAAAAAAGGAGGTGCCCTGATGAGCGAAAAAAAAAAAAAAAAAGCAGTGAaaaaat                                                                  >  2:1560762/1‑138 (MQ=255)                                                                           tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAgaga                                                         <  1:1560762/140‑1 (MQ=255)                                                                            atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGAt                                                        <  1:758595/140‑1 (MQ=255)                                                                            atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGAt                                                        <  1:336839/140‑1 (MQ=255)                                                                              tCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑T‑TATTTTTT‑CAGAC‑AAAAACAAAAAATGGAGTTGCCATGATTGGAGGAAGTAATAAAAAAAAAGCAGCGAATAAAATGAAAgagaatt                                                      >  2:336839/1‑137 (MQ=255)                                                                              tCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GATTTTTT‑CCGAA‑AAAAAAAAAAAATGGAGGTGGCATGATGAGCGAAAGAAAAAAAAAAAAAGCAGTGAAAAAATTTACAGAGAATg                                                      >  2:1129056/1‑140 (MQ=255)                                                                                  ggTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGc                                                  <  1:143747/140‑1 (MQ=255)                                                                                      gCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑GAATTTTT‑CAGACAAAAAAAAAAAAAGGGGGTTGCC‑TGATGAGGGGAAAGAAAAAAAAAAAAGCAGGGAATAAAATGACAAAGAATGTCGCTaaa                                              >  2:963484/1‑139 (MQ=255)                                                                                          aaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACGGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTa                                          <  1:916241/140‑1 (MQ=255)                                                                                           aaaTATAAAACCACATTTTTAGTGGTATTTTGGGGCGGT‑A‑AATTTTTC‑CAGAC‑AAATACAAAACCTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTAc                                         <  2:374067/140‑1 (MQ=255)                                                                                            aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAcc                                        <  1:31402/140‑1 (MQ=255)                                                                                                        caTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTT‑CAAAC‑AAAAACAAAAAATGGGGGTGGCCTGATGAGCGGAAAAAAAAAAAAAAAAGCAGTGAATAAATTGACAGAGATTGTCGCTAAATTTTACGCCATGAttttt                            >  2:1429199/1‑138 (MQ=255)                                                                                                             ttAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCg                       <  1:997410/140‑1 (MQ=255)                                                                                                             ttAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCg                       <  1:1681969/140‑1 (MQ=255)                                                                                                               ggtggtgTTTTGGGGCGGT‑A‑ATTTTTTC‑AAGAA‑AAAAAAAAAAACTGGAGTTGCCTTGATGAGCAAAAGTAAAAAGCAACAGGAAGTAAATAAGTTGACAGAGATTGTCGTTAATTTTACCGCCATGATTTCTACCCGaa                     <  2:445602/139‑1 (MQ=255)                                                                                                               agacagaGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                     <  1:71342/134‑1 (MQ=255)                                                                                                               aGTGGTTGTTTGGGGGGGT‑A‑ATTTTTTC‑CAAAA‑AAATAAAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGAAAAAGGCAGTAAATAAGTTGACAGAGTTTGTCGCTACTTTTACCGCCATGATTTCTACCCGaa                     <  2:1808666/140‑1 (MQ=255)                                                                                                               aGTGGTAGTTTGTGGCGGT‑GTAATTTTTCTCAGCA‑AAATAAAAAAA‑‑AGAGATGCCATGGTCGACGAAAGGAAAAAGCAAACGGCAGTGAAAAACCTGAGAGAGAGTGTTGTGAACTTTAACCCCCTGGTTTTTACCCaaa                     >  2:1371460/1‑140 (MQ=255)                                                                                                                       tttGTGGCGGT‑G‑AATTTTTT‑CAGAC‑AAAAACAAAAAATGGGGGTGGCCTGATGAGCGAAAGAAATAAACAACAAGCAGTGAATAAATTGAAAGAGATTGTCGCTAAATTTTCCGCCCTGATTTTTACCCCAATGCCtgat             >  2:1681969/1‑140 (MQ=255)                                                                                                                       tttGTGGCGGT‑G‑AATTTTTT‑CAGAC‑AAAAACAAAAAATGGGGGTGCCATGATGAGCGAAAGTAATAAACAAAAAGCAGGGAATAAATTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTTTACCCCAATGCCtgat             >  2:997410/1‑140 (MQ=255)                                                                                                                             gCGGT‑G‑AATTTTTC‑CAAAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg       <  2:1033385/140‑1 (MQ=255)                                                                                                                                gT‑G‑AATTTTTT‑CAGAC‑AAAAACAAAAAAAGGAGGTGCCATGATGAGCGAAAGGAATAAACAAAAAGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCCTGATTTTTACCCCCATGCCTGATGACctgtct    >  2:71342/1‑137 (MQ=255)                                                                                                                                gT‑G‑AATTTTTT‑CAGAC‑AAAAAAAAAAAATGGAGTTGCCATGATGAGCGGAAGTAAAAAACAACAGGCAGTGAATAAATTGACAGAGAATGTCGCTAACTTTTCCGCCATGATTTTTACCCGAAAGCCTGATGACgtgggg    >  2:1288865/1‑138 (MQ=255)                                                                                                                                   g‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa  <  1:1288865/140‑1 (MQ=255)                                                                                                                                            |                                                                                                                                      AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTC‑CAGAC‑AAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206298‑3206566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑