Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	29.0%	47.7 / 14.4	31	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (4/18);  new base T (9/0);  total (13/18)
Fisher's exact test for biased strand distribution p-value = 3.55e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206298‑3206574                                                                                                                                          |                                                                                                                                             aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCa                                                                                                                                            >  2:669760/1‑140 (MQ=255) aaaaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCa                                                                                                                                            >  2:656357/1‑140 (MQ=255)     cATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACa                                                                                                                                        <  2:79602/140‑1 (MQ=255)          ccATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATAc                                                                                                                                   <  2:398624/140‑1 (MQ=255)               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAaaaaaaaaaaaaaa                                                                                                                              >  1:945541/1‑140 (MQ=255)                    ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAaaaaaaaaaaaagga                                                                                                                         >  2:875515/1‑135 (MQ=255)                    ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCACACAaaaaaaaaaaattga                                                                                                                         >  1:653817/1‑135 (MQ=255)                         gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAATACAAAAACTGGA‑GTTGc                                                                                                                   >  1:214017/1‑140 (MQ=255)                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGcc                                                                                                                  <  2:53635/140‑1 (MQ=255)                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAg                                                                                                          <  1:669760/140‑1 (MQ=255)                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAg                                                                                                          <  1:656357/140‑1 (MQ=255)                                         tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCCTACAAAAACAAAAAATGGA‑GTTGGCATGATGAGCGAAAga                                                                                                   >  2:1058726/1‑139 (MQ=255)                                         tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAATGGA‑GGTGCCCTGATGAGGGAAAGt                                                                                                   >  1:695975/1‑140 (MQ=255)                                         tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAACGCAATAAAAAAAACAGA‑GATTCCATGATATGGGAAAga                                                                                                   >  1:630416/1‑139 (MQ=255)                                         tATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGGGAAATTTTTCAAACAAAAAAAAAAAAAGGA‑GGTGTCCTGATGAGGGaaaaa                                                                                                   >  2:1027337/1‑138 (MQ=255)                                                   ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                         <  1:1124903/140‑1 (MQ=255)                                                   ttGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAAc                                                                                         <  2:591726/140‑1 (MQ=255)                                                              aCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAAAAAAAAAAGGA‑GGTGGCATGATGAGGGGAAAAAAAAAACAAAAAGCAGGGaaa                                                                              >  2:1014146/1‑139 (MQ=255)                                                               cTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATa                                                                             <  1:804393/140‑1 (MQ=255)                                                                        aCATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGA‑GGTGGCATGATGAGCGAAAAGAATAAAAAAAAAGCAGTGAATAAATTGACag                                                                    >  2:388199/1‑140 (MQ=255)                                                                                   gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                         <  2:1060558/140‑1 (MQ=255)                                                                                    tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATGGAGGTTGCC‑TTATGAGGGGAAAGAAAAAACAAAAAGCAGGGAATAAATTTGCAGAGAATGTTGCTa                                                        >  2:1010313/1‑140 (MQ=255)                                                                                      gCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTTCAAACAAAAAAAAAAAATGGA‑GGTGGCCTGATGAGGGAAAGAAATAAACAAAAAGCAAAGAAAAAAATGAAAGAGAATTTCGCTaaa                                                      >  2:617763/1‑139 (MQ=255)                                                                                          aaaaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTa                                                  <  1:1014146/140‑1 (MQ=255)                                                                                            aaTATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTAcc                                                <  2:414476/140‑1 (MQ=255)                                                                                                aaaaaCCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCa                                            <  1:1058726/139‑1 (MQ=255)                                                                                                 aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCAt                                           <  2:214017/140‑1 (MQ=255)                                                                                                 aaaaCCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACGGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACGGGAAGTGAATAAGTTGACAGAGATTGTCGCTAATTTTACCGCCAt                                           <  2:945541/140‑1 (MQ=255)                                                                                                      cacaTTTTTAGTGGTAGTTTGTGGCGGTGGATTTTTTCAGACAAAAACAAAAAATGGA‑GGTGGCATGATGAGCGAAAGGAATAAACAACAAGCAGGGAATAAGTTGACAGAGAATGTCGCTAACTTTACCGCCATGAttt                                      >  2:692424/1‑140 (MQ=255)                                                                                                                gTGGTAGTTTGTGGCGGTGAATTTTTTCAGACAAAAACAAAAAATGGG‑GGTGTCCTGATGAGCGAAAGTAATAAACAAAAGGCAGGGAATAAATTGACAAAGATTGTCGCTAACTTTTCCGCCAAGATTTTTACCCCAAt                            >  2:386733/1‑140 (MQ=255)                                                                                                                        ttGTGGGGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                    <  1:412955/140‑1 (MQ=255)                                                                                                                        ttGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                    <  1:875515/140‑1 (MQ=255)                                                                                                                          gtgGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCAAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGAc                  <  1:617763/140‑1 (MQ=255)                                                                                                                                gTGAATTTTTTCAGAAAAAAACAAAAAATGGA‑GGTGCCCTGATGAGGGAAAGTAAAAAGCAAAAGGCAGTGAATAAAATGACAGAGATTGTTCCTAACTTTACCCCCCTGATTTCTACCCGAATGCCTGATGACgggggg            >  2:313709/1‑138 (MQ=255)                                                                                                                                  gAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  1:388199/140‑1 (MQ=255)                                                                                                                                  gAATTTTTCCAGAAAAATACAAAAACGGGA‑GTTGCCATGATGAGCGAAAGTAAAAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  2:695975/140‑1 (MQ=255)                                                                                                                                  cattttttCGAGACAAATAAAAAAACTGGA‑GTTGCAATGATGAGCGAAAGAAAAAAGCAACAGGCAGTGAATAAGTTAACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  2:346034/137‑1 (MQ=255)                                                                                                                                  aatttttaCCAAAAAAAAACAAAAACGGGA‑GTTGCCATGAGGAGCAAAAGAAATAACCAACGGGCAGTAAATAGGTTGAAAGAGATTTGCGCTATCTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGa          <  2:630416/137‑1 (MQ=255)                                                                                                                                        ttCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAGTAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACt    >  2:1043463/1‑140 (MQ=255)                                                                                                                                        ttCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACt    >  2:787674/1‑140 (MQ=255)                                                                                                                                          ccAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTaa  >  2:674151/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                             AAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGAATTTTTCCAGACAAATACAAAAACTGGA‑GTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTAA  >  NC_000913/3206298‑3206574

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: ‑