Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	28.9%	75.2 / 21.1	45	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (1/31);  new base T (13/0);  total (14/31)
Fisher's exact test for biased strand distribution p-value = 1.92e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206300‑3206574                                                                                                                                        |                                                                                                                                             aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCata                                                                                                                                          >  2:537959/1‑138 (MQ=255)      tGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAGAaaaaa                                                                                                                                     >  2:183958/1‑139 (MQ=255)        ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCCCATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATAc                                                                                                                                   <  1:95154/140‑1 (MQ=255)        ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATAc                                                                                                                                   <  1:607449/140‑1 (MQ=255)             cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAGAcaaaaacaaaaa                                                                                                                              >  2:1189571/1‑140 (MQ=255)              ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAAATTTTTCTGAAAAAAACaaaaaa                                                                                                                             >  2:1105511/1‑139 (MQ=255)                tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAACTg                                                                                                                           >  1:211320/1‑140 (MQ=255)                tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATAAAAAAAATg                                                                                                                           >  1:666878/1‑140 (MQ=255)                tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTg                                                                                                                           <  2:942584/140‑1 (MQ=255)                 gCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTAC‑‑ATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                        <  2:952083/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                        <  1:753738/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                        <  2:584514/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                        <  2:122805/140‑1 (MQ=255)                   tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                        <  1:183958/140‑1 (MQ=255)                            atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCACAAAAAAAAAAAAAATGGAGGTGCCatga                                                                                                               >  2:83408/1‑140 (MQ=255)                            atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATGGAGTTGCCctga                                                                                                               >  2:753738/1‑140 (MQ=255)                                   ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                        <  1:418704/140‑1 (MQ=255)                                   ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                        <  1:1183488/140‑1 (MQ=255)                                   ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                        <  1:935007/140‑1 (MQ=255)                                   ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                        <  1:537959/140‑1 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCCAACAAAAACAAAAAATGGAGGTGCCATGATGAGCGAAAga                                                                                                    >  2:490268/1‑139 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAACAAAAAACGGAGGTGGCATGATGAGGGAAAga                                                                                                    >  2:202631/1‑139 (MQ=255)                                       tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAATTTTTTCAGACAAAAACAAAAAAAGGGGTTGGCCTGATGAGCGAAAga                                                                                                    >  2:935007/1‑139 (MQ=255)                                        aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGTTGCCATGATGAGCGAAAAta                                                                                                   >  1:675364/1‑140 (MQ=255)                                        aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGta                                                                                                   <  1:968378/140‑1 (MQ=255)                                          tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                                 <  2:211320/140‑1 (MQ=255)                                          tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                                 <  2:705455/140‑1 (MQ=255)                                                 ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                          <  1:728924/140‑1 (MQ=255)                                                    aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                       <  1:82407/140‑1 (MQ=255)                                                    aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                       <  1:691796/140‑1 (MQ=255)                                                    aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                       <  2:500795/140‑1 (MQ=255)                                                    aTTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAgg                                                                                       <  1:260760/140‑1 (MQ=255)                                                     ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                      <  1:83408/140‑1 (MQ=255)                                                            aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATAGAGGTGGCATTATTAGCGGAAAAAAAAAACAAAAAGCAGGGaaa                                                                               >  2:82407/1‑139 (MQ=255)                                                              tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATaa                                                                             <  1:73267/140‑1 (MQ=255)                                                               gTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                            <  1:931258/140‑1 (MQ=255)                                                                ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGt                                                                           <  1:490268/140‑1 (MQ=255)                                                                              aCGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAAATTTTTCAGACAAAAAAAAAAAAAGGGGGTGCCATGATGAGCGGAAGAAATAAAAAAAAAGCAGGGAATAAGATGACAGAGATTGtg                                                             >  2:264447/1‑139 (MQ=255)                                                                                     cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAGACAAAAAAAAAAAAAGGAGGTTCCATGATGAGGGAAAATAATAAACAAAAAGCAGTGAATAAATTGAGAGAGAATTTTGCT‑aaat                                                     >  2:526757/1‑138 (MQ=255)                                                                                         aaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑ACCTTTAc                                                 <  2:600988/140‑1 (MQ=255)                                                                                                     acaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTc                                     <  2:675364/140‑1 (MQ=255)                                                                                                      caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAAAGGGGTTGCCAAGATGAGGGAAAAAAAAAAAAAAAAAGCAGGGAAAAAATTGACAAAGATTTTTGCT‑AACTTTATCGCCCTGAttttt                                    >  2:431623/1‑138 (MQ=255)                                                                                                      caTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGAAAAAAAAAAAAAATGGAGGTGGCATGATGAGGGGAAAAAATAAACAAAAAGCAGTGAATAAATTGACAGAGAATGTTGCTAAACTTTACC‑CCATGAttttt                                    >  2:1009808/1‑138 (MQ=255)                                                                                                      aaTTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCAAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTAAATAAGTTAACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCt                                    <  2:666878/139‑1 (MQ=255)                                                                                                            tAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGa                              <  1:264447/140‑1 (MQ=255)                                                                                                             aGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGAGGTGGCATGATGAGCGAAAAAAAAAAACAACAAGCAGAGAAAAAATTTACAGAGAATGTCGCT‑AACTTTACCCCCATGATTTTTACCCGaa                             >  2:848104/1‑140 (MQ=255)                                                                                                                ggTAGTTTGTGGCGGTGAATTTTTTCACACAAAAATAAAAACATGAGGTGGCATGATGAGCGAAAGGAATAAGCAACAAGCAGTGAATAAGTTGTCAGAGAATGTCGCT‑AACTTTACCGCCATGATTTCTATCCCAATGc                          >  2:483569/1‑140 (MQ=255)                                                                                                                      ttGTGGGGGTGAATTTTTCAAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGGGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                    <  1:526757/140‑1 (MQ=255)                                                                                                                      ggggggCGGTGAATTTTTCCAGAAAAATAAAAAAACGGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑ATTTTTACCGCCATGATTTCTACCCGAATGCCtgatg                    <  2:1010066/136‑1 (MQ=255)                                                                                                                           gCGGTGAATTTTTCCAGACAAATAAAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACgtg               <  1:1189571/140‑1 (MQ=255)                                                                                                                                gAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  1:35862/140‑1 (MQ=255)                                                                                                                                gAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAAAAAGCAACAGGCGGTAAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  1:483569/140‑1 (MQ=255)                                                                                                                                gAATTTTTCCAGAAAAATACAAAACCTGGAGTTGCCATGAGGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  1:1105511/140‑1 (MQ=255)                                                                                                                                 aaTTTTTTCAGACAAAAACAAAAAATGGAGGTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTAACGCCCTGATTTTTTCCCGAATGCCTGATGACGgggggggt         >  2:35862/1‑138 (MQ=255)                                                                                                                                   tttttCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGAtct       >  1:1010066/1‑138 (MQ=255)                                                                                                                                        ccAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaa  <  1:19016/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                             AACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCT‑AACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206300‑3206574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑