Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	24.3%	73.6 / 11.9	37	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (0/28);  new base T (9/0);  total (9/28)
Fisher's exact test for biased strand distribution p-value = 8.04e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206296‑3206566                                                                                                                                             |                                                                                                                                     gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTc                                                                                                                                      <  2:972268/140‑1 (MQ=255)   aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCa                                                                                                                                    <  1:98544/140‑1 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGa                                                                                                                                  <  2:241481/140‑1 (MQ=255)          tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGGAATTTTTTCA‑ACa‑aaa                                                                                                                            >  2:429164/1‑139 (MQ=255)          tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACa‑aaa                                                                                                                            >  1:287914/1‑139 (MQ=255)            ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATAc                                                                                                                          <  1:562548/140‑1 (MQ=255)            ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATAc                                                                                                                          <  2:394674/140‑1 (MQ=255)                  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAAc                                                                                                                    <  2:70858/140‑1 (MQ=255)                  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAAc                                                                                                                    <  2:1203004/140‑1 (MQ=255)                  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAAc                                                                                                                    <  2:443334/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAg                                                                                                               <  2:190319/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAg                                                                                                               <  2:539928/140‑1 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGAGCAGTTTTCCAGGAC‑AACAAAAAAACTggcatttc                                                                                                           >  1:419919/1‑134 (MQ=255)                              cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACACAAAAAAAAAAATGAGGTTGcct                                                                                                         >  1:49956/1‑139 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                               <  1:935220/140‑1 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                               <  2:1036890/140‑1 (MQ=255)                                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCCGACA‑AAAAAAAAAAATGGGGGTGCCCTGATGAGCGGAAga                                                                                           >  1:519319/1‑139 (MQ=255)                                           tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACA‑AAAAAAAAAAAAGGAGGTGGCGTGATGAGCGAAAga                                                                                           >  1:689080/1‑139 (MQ=255)                                              tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                        <  1:670405/140‑1 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAAACA‑AAAAAAAAAAATGGAGTTGGCATGATGAGCGGAAGGAAAAAacaacaag                                                                              >  1:1140062/1‑138 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  1:556188/140‑1 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  2:700043/140‑1 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  2:7950/140‑1 (MQ=255)                                                        aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                              <  1:679006/140‑1 (MQ=255)                                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                             <  2:287914/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                       <  1:637446/140‑1 (MQ=255)                                                                 cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                     <  1:333809/140‑1 (MQ=255)                                                                  tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTTAAAAA‑AAAAAAAAAAAAGGAGGTGTCCTTAGGAGCGAAAGGAATAAACAAAAAGCAGTGAaaaa                                                                    >  2:186738/1‑140 (MQ=255)                                                                    ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAAATTTTTCAGACA‑AAAAAAAAAAATAGAGTTGGCATGGTGAGGGGAAGTAATAAAAAAAAAGCAGAGAaaaaat                                                                  >  2:650750/1‑138 (MQ=255)                                                                     tAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGtt                                                                 <  2:94917/140‑1 (MQ=255)                                                                       aTTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGa                                                               <  2:961344/140‑1 (MQ=255)                                                                             tatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAgaga                                                         <  2:1120560/140‑1 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTTCAGACA‑AAAACAAAAAATGGAGGTGGCATGGTGAGGGGAAAGAATAAAAAAAAAGGAGTGAAAAAATTGAAAgagaa                                                        >  2:979257/1‑139 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGAt                                                        <  2:722936/140‑1 (MQ=255)                                                                                      tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAAATTTTTCCGACA‑AAAAAAAAAAATGGAGGTTTTCTGTTGGGAGGAAAAAATAAAAAAAAAACAGTGAATAAAATTACAGAGATTGTCGCTa                                                >  2:59565/1‑140 (MQ=255)                                                                                          aaaaaaTATAAAACCACATTTTTAGTGGTATTTTGTGGG‑GGTGAATTTTTCAAGAAA‑AATAAAAAAACGGGAGTTGCCATGATGAGCAAAAGTAAAAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAAttt                                            <  2:578640/140‑1 (MQ=255)                                                                                            aaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTa                                          <  2:477429/140‑1 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGC‑GGTGGATTTTTTCAGACA‑AAAAAAAAAAATGGAGGTGCCCTGGTGAGCGGAAGAAATAAACAAAAAGCAGTGAAAAAAGTGAAAGAGATTGTTGCTAAATTTTCCGCCCTGAttttt                            >  2:658103/1‑138 (MQ=255)                                                                                                                tAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGAAA‑AAAACAAAAACGGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGa                      <  2:1079593/140‑1 (MQ=255)                                                                                                                tAGTGGTAGTTTGTGGC‑GGTAAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGa                      <  2:443147/140‑1 (MQ=255)                                                                                                                 aGTGGTAGTTTGGGGG‑GGGGAATTTTTCCAGAAA‑AATAAAAAAACTGAAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTTAAAAAGTTGACAAAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                     <  2:49956/140‑1 (MQ=255)                                                                                                                  gTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                    <  1:979257/140‑1 (MQ=255)                                                                                                                  gTGGTAGTTTGTGGC‑GGTGAATTTTTCCAAAAA‑AAAACAAAAACTGGAGTTCCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAAt                    <  2:164939/140‑1 (MQ=255)                                                                                                                     gTAGTTTGTGGC‑GGTGAAATTTTTCAGACA‑AAAACAAAAAATGGAGTTGCCATGGTGAGCGAAAGGAATAAGAAAAAAGCAGTGAAAAAATTGACAGAGATTTTCGCTAAAATTACCGCCATGAATTTTACCCGAAAGcc                 >  2:177529/1‑140 (MQ=255)                                                                                                                     gTAGTTTGTGGC‑GGCGGAGTTTTTCCCACA‑AAAAACAAAAATGGAGATGCCATGATGAGGGGAAAAAATAAGAAAAAAGCAGTGAAAAAATTGACCGAAAATGGCGCCAAATTTACCGCCATGATTTCTACCCGGATAcc                 >  2:158051/1‑140 (MQ=255)                                                                                                                          ttGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg            <  1:658103/140‑1 (MQ=255)                                                                                                                          ttGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg            <  1:650750/140‑1 (MQ=255)                                                                                                                          ttGTGGC‑GGTGAATTTTTCAAAAAA‑AATACAAAAACTGGAGTTGCCATGATGAGAGAAAGTAATAACCACCAGGCAGTAAAAAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg            <  2:391471/140‑1 (MQ=255)                                                                                                                                   gTGAATTTTTTCAGACA‑AATACAAAAAATGGAGGTGGCCTGATGAGCGAAAGGAATAAGCAAAAAGCAGTGAATAAATTTACAGAGATTGTCGCTAACTTTACCGCCATGATTTTTACCCCAATGCCTGATGACgtgggg    >  2:459813/1‑138 (MQ=255)                                                                                                                                   gTGAATTTTTTCAGACA‑AAAACAAAAAATGGAGGTGCCATGATGAGCGAAAGTAATAAACAAAAAGCAGGGAATAAGTTGACAGAGATTGTCGCTAAATTTACCGCCATGATTTTTACCCGAATGCCTGATTACgtggtg    >  2:998655/1‑140 (MQ=255)                                                                                                                                    tGAATTTTTTCAGACA‑AAAAAAAAAAATGGAGTTGGCATGATGAGGGAAAGTAATAAACAAAAAGCAGTGAATAAATTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGtggtgg   >  2:318051/1‑140 (MQ=255)                                                                                                                                     aaaTTTTTCAAAAAA‑AAAAAAAAATCTGGAGTTGCGATTAAGAGACAAAATAATAAGCAACAGGCAGGGAATAAGTTCACAGAGATGGCGGAAATCTTAACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa  <  2:679961/139‑1 (MQ=255)                                                                                                                                             |                                                                                                                                     GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGC‑GGTGAATTTTTCCAGACA‑AATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGA  >  NC_000913/3206296‑3206566

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑