Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	24.4%	80.3 / 14.7	41	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (3/28);  new base T (10/0);  total (13/28)
Fisher's exact test for biased strand distribution p-value = 2.55e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206296‑3206574                                                                                                                                              |                                                                                                                                            gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATACTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTc                                                                                                                                             <  2:321980/140‑1 (MQ=255)   aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCa                                                                                                                                           >  1:1220060/1‑140 (MQ=255)   aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCa                                                                                                                                           >  1:494044/1‑140 (MQ=255)   aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCa                                                                                                                                           >  1:15508/1‑140 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTTCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑GAAATTTTTccga                                                                                                                                          >  2:1341771/1‑138 (MQ=255)      aCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGAc                                                                                                                                        <  2:1054777/140‑1 (MQ=255)       cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACa                                                                                                                                       <  1:111916/140‑1 (MQ=255)       cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACa                                                                                                                                       <  1:386209/140‑1 (MQ=255)                    tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTg                                                                                                                          <  2:870462/140‑1 (MQ=255)                      ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGa                                                                                                                        <  1:274249/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAg                                                                                                                       <  2:652724/140‑1 (MQ=255)                         tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATACAAAAACTGGAGtt                                                                                                                     >  1:830561/1‑140 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACaaaa                                                                                                                                    >  2:1289703/1‑122 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAATGGAGTTGc                                                                                                                   >  2:1132234/1‑140 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAAAAGAGTTgg                                                                                                                   >  2:1364532/1‑139 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAAt                                                                                                                                    <  1:1289703/123‑1 (MQ=255)                              cAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCat                                                                                                                <  2:36402/140‑1 (MQ=255)                               aaTATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatg                                                                                                               <  1:1355173/140‑1 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTTCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatga                                                                                                              <  1:1341771/140‑1 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCatga                                                                                                              <  2:684269/140‑1 (MQ=255)                                    tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAg                                                                                                          <  1:409641/140‑1 (MQ=255)                                     cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGAAAAAAACAAAAAATGGAGTTTGCATGAagagg                                                                                                         >  1:484741/1‑139 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                       <  2:428509/140‑1 (MQ=255)                                        tcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAACAAAAAATGGAGGTGGCATGATGAgggga                                                                                                      >  1:640559/1‑136 (MQ=255)                                              tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                                <  2:494044/140‑1 (MQ=255)                                               ttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGG‑AATTTTTTC‑GACAAATACAAAAAAACGAGTGGTGATGATGGGGGAAAGgaata                                                                                               >  2:401195/1‑140 (MQ=255)                                                tCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaataa                                                                                              <  2:830561/140‑1 (MQ=255)                                                 cgcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAg                                                                                             <  1:157579/140‑1 (MQ=255)                                                  gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑GATTTTTTCAAACAAAAAAAAAAAAAGGGGGTGGCATGATGAGGGAAAGaaataaaa                                                                                            >  2:157579/1‑138 (MQ=255)                                                  gcgTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGG‑G‑AATTTTTTTCAACAAAAAAAAAAAATTGAGTTGCCATGATGAGGGGAAAtaataaaa                                                                                            >  1:1037693/1‑138 (MQ=255)                                                    gTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCaa                                                                                          <  1:33557/140‑1 (MQ=255)                                                     ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                         <  1:263813/140‑1 (MQ=255)                                                      tGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACa                                                                                        <  1:22796/140‑1 (MQ=255)                                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                     <  1:1003316/140‑1 (MQ=255)                                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                     <  1:52198/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                               <  2:15508/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTACAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                               <  2:1069306/140‑1 (MQ=255)                                                                    ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACA‑TTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAAATGGAGATGCCATGATGAGCGAAAGTAATAAGCAACAGGAAATGGATAAGtt                                                                         >  1:803545/1‑140 (MQ=255)                                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AAATTTTTCAGACAAAAACAAAAAATTGAGGTGGCCTGATGAGGGAAAATAAAAAACAACAAGCAGGGAAAAAATTGAAAGAGATTGTCggt                                                         >  2:78566/1‑138 (MQ=255)                                                                                      tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTa                                                        <  2:1410889/140‑1 (MQ=255)                                                                                              aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAcc                                                <  2:825775/140‑1 (MQ=255)                                                                                                tataAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAATGGAGGTGGCATGATGAGGGAAAGGAAAAAACAACAAGCAGGGAATAAAATGACAGAGATTGTCGCTAACTTTATCGc                                              >  2:865960/1‑140 (MQ=255)                                                                                                  aaaaaCCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATAAAAAAACTGGATTTGCAATGAGGAGCGAAAGAAATAAGCAACAGGCAGTAAATAAGTTGAAAGAAATTGCCGCTAACTTTACCGCCa                                            <  2:1125479/139‑1 (MQ=255)                                                                                                          caTTTTTAGTGGTATTTTGTGGCGGT‑A‑AATTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAACAACAGGCAGTGAATAAGTGGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCt                                    <  2:640559/140‑1 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGACAAAAACAAAAAAAGGAGGGGGCCTGATGAGGGGAAGAAAAAAAAAAAAAGAAGGGAAAAAAATGACAGAGATTGTCGCTAAATTTACCGCCCTGAttttt                                    >  2:1379204/1‑138 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCCGACAAAAAAAAAAAATAGAGGTGCCATGATGAGGGGAAGTAAAAAAAAAAAAGCAGTGAAAAAAATGAAAGAGAATGTCGCTAAATTTAACCCCACGAttttt                                    >  2:851723/1‑138 (MQ=255)                                                                                                          caTTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAATAAAAAAAATGGAGTTGCCATGATGAGCGAAAGGAATAAGAAACAGGCAGTGAATAAATTTAAAGAGATTTTCGCTTAATTTTCCGCCATGAttttt                                    >  2:1175922/1‑138 (MQ=255)                                                                                                                tAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGa                              <  1:865960/140‑1 (MQ=255)                                                                                                                 aGTGTTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                             <  2:123675/140‑1 (MQ=255)                                                                                                                     gTAGTTTGTGGCGGT‑G‑AATTTTTTCAGACAAAAAAAAAAAATGGGGGTGGCATGATGAGGGGAAGTAATAAACAAAAAGCAGGGAATAAATTGACAGAGATTGTCGCTAACTTTTTCGCCCTGATTTTTACCCCaaaacc                         >  2:471571/1‑136 (MQ=255)                                                                                                                     gTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGcc                         <  1:1379204/140‑1 (MQ=255)                                                                                                                          ttGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTAGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                    <  1:851723/140‑1 (MQ=255)                                                                                                                                      aaaTTTTTCCAGAAAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAGGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  2:484741/139‑1 (MQ=255)                                                                                                                                              ccAGAAAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGTTTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaa  <  1:1364532/140‑1 (MQ=255)                                                                                                                                              |                                                                                                                                            GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGT‑G‑AATTTTTCCAGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206296‑3206574

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑