Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,206,435	0	C	T	31.6%	55.6 / 19.9	38	intergenic (‑179/‑28)	ttdR/ttdA	DNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
Reads supporting (aligned to +/- strand):  ref base C (3/23);  new base T (12/0);  total (15/23)
Fisher's exact test for biased strand distribution p-value = 1.68e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTA  >  NC_000913/3206296‑3206573                                                                                                                                             |                                                                                                                                            gCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTc                                                                                                                                             >  1:369221/1‑140 (MQ=255)     aaCATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGa                                                                                                                                        >  2:758663/1‑140 (MQ=255)             cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACa                                                                                                                                <  2:448584/140‑1 (MQ=255)                  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAAc                                                                                                                           <  1:18398/140‑1 (MQ=255)                  ccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGCGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAAc                                                                                                                           <  1:76301/140‑1 (MQ=255)                    tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑GATTTTTTC‑ACAAAAAAACaaaaaaaa                                                                                                                         >  2:643692/1‑137 (MQ=255)                    tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑AGAcaaaaacaaaaaaag                                                                                                                         >  1:445298/1‑137 (MQ=255)                    tGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGCG‑GATTTTTTC‑CGACAAATACAAAAAATg                                                                                                                         >  1:1057425/1‑140 (MQ=255)                      ctctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGa                                                                                                                       <  2:369221/140‑1 (MQ=255)                       tctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAg                                                                                                                      <  1:758663/140‑1 (MQ=255)                         tGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AAATTTTTC‑AGACAAAAAAAAAAAAAGGAggt                                                                                                                    >  2:36094/1‑138 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑AGACAGATACAAAAAATGGAGGTGc                                                                                                                  >  2:1162634/1‑140 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑AGACAAAAAAAAAAAATGGAGTTGc                                                                                                                  >  2:428124/1‑140 (MQ=255)                           gcgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACAGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑GATTTTTTC‑AAACAAAAAAAAAAAAAGGAGGTgg                                                                                                                  >  2:508706/1‑139 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCatga                                                                                                             <  2:235340/140‑1 (MQ=255)                                atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCatga                                                                                                             <  1:310928/140‑1 (MQ=255)                                     cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑CGACAAAAAAAAAAAATGGAGTTGTCATGATGAgg                                                                                                        >  2:310928/1‑139 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAGATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                      <  1:1162634/140‑1 (MQ=255)                                       ttcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGa                                                                                                      <  1:518277/140‑1 (MQ=255)                                          ttATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAg                                                                                                   <  1:428124/140‑1 (MQ=255)                                            aTTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGta                                                                                                 <  1:1152896/140‑1 (MQ=255)                                             ttttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑GATTTTTTC‑CAAAAAAAAAAAAAACTGGAGGTGCCAAGATGAGGggaaggaa                                                                                                >  2:518277/1‑140 (MQ=255)                                              tttCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGtaat                                                                                               <  2:57102/140‑1 (MQ=255)                                                       gATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑AAACAAAAACAAAAACATGAGTTGCCCTGATTAGCGAAAGTAAAAAGCAACaa                                                                                      >  1:849416/1‑139 (MQ=255)                                                         ttCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGc                                                                                    <  1:1198588/140‑1 (MQ=255)                                                               aaCTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGaa                                                                              <  1:1256681/140‑1 (MQ=255)                                                                  tGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATaa                                                                           <  1:36094/140‑1 (MQ=255)                                                                   gTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAg                                                                          <  1:955055/140‑1 (MQ=255)                                                                    ttAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑AGAAAAATAAAAAAAATGGAGGTGGCATGATGTGGGAAAGTAAAAAACAAAAAGCAGAGAATAAGt                                                                         >  2:1198588/1‑140 (MQ=255)                                                                     tAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGtt                                                                        <  2:1416071/140‑1 (MQ=255)                                                                            atatTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGAT‑AATTTTTTC‑AGACAAATAAAAAAAAATGAGTTTTCCTGATGAACGGAAGTAAAAAACAACAAGCAATGAATAAATTTAAagaa                                                                 >  2:647488/1‑139 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTTC‑CCACAAAAATAAAAAAAAGAGGTGCCATGATGAGAGAAAAAAAAAAGAAAAAAACACAGAAAAAATTGAAAgagaa                                                               >  2:651431/1‑139 (MQ=255)                                                                              atTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AAATTTTTT‑AGACAAAAAAAAAAAAAGGAGGTGGCATGATGAGAGAAAAGAAAAAAAAAAAAGGAGAGAAAAAGTTGAGAAAGAt                                                               >  2:177174/1‑140 (MQ=255)                                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                        <  1:1062932/140‑1 (MQ=255)                                                                                     gTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AAATTTTTC‑AAACAAAAAAAAAAAATGGGGTTGCCATGATGAGGGAAAGTAAAAAACAAAAAGCAGTGAAAAAAATGACAGAGATTGTCGcc                                                        >  2:679/1‑139 (MQ=255)                                                                                     gTGGAAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCt                                                        <  1:626314/140‑1 (MQ=255)                                                                                      tGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑GAATTTTTT‑AGACAAAAAAAAAAAAAGGAGGTGGCCTGATGAGCGAAAAGAAAAAAAAAAAAGCAGTGAAAAAAATGAAAAAGAATGTTGCTa                                                       >  2:1062932/1‑140 (MQ=255)                                                                                         cAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTGTAATTTTCTC‑ACGCAAA‑ACAAAAACTAGCGAGTGCATGGAGAGGGGGAAGAATAAACAAAAAGGAGGGAAAAAATTGACAGAGATTTTTGCTTACt                                                    >  2:106983/1‑140 (MQ=255)                                                                                                  aaaacCCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCa                                           <  1:643692/139‑1 (MQ=255)                                                                                                  aaaacCCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATAAAAAAACGGGAGTTGCCATGATGAGCGAAAGAAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCCCTAACTTTACCGCCa                                           <  2:849416/139‑1 (MQ=255)                                                                                                     aaCCACATTTTTAGTGGTAGTTTGTGGCGGGG‑AAATTTTTC‑AAACAAAAAAAAAAAAAGGGGTTGGCCTGATTAGCGAAAAAAAAAAACAAAAGGCAAGGAAAAAAATGAAAGAGAATGTCGCTAACTTTATCCCCATGa                                        >  2:982852/1‑140 (MQ=255)                                                                                                                 ggTGGTAGTTTGTGGGGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGAGGAGCGAAAATAATAAGCAACAGGCAGAAAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGaa                            <  1:647488/139‑1 (MQ=255)                                                                                                                    ggTAGTTTGTGGCGGTG‑AATTTTTTC‑AGACAAAAAAAAAAAATGGAGGTGGCATGATGAGGGGAAGGAAAAAACAACAAGCAGGGAAAAAATTGACAGAGATTGTTGCTAACTTTACCCCCCTGATTTTTTCCCCAATGc                         >  2:612538/1‑140 (MQ=255)                                                                                                                       aGTTTGTGGCGGTG‑AATTTTCCC‑AGACAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTAAATAAGTTAACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtg                      <  2:595379/140‑1 (MQ=255)                                                                                                                          ttGTGGGGGTA‑AATTTTTCC‑AGACAAATAAAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCACCAGGCAGTGAATAAGTTGACAGAGATTGTCGCTATCTTTACCGCCATGATTTCTACCCGAATGCCtgatg                   <  2:665567/140‑1 (MQ=255)                                                                                                                          ttGTGGCGGT‑‑AATTTTTCCAAAAAAAAAAAAAAAACTGGAGTCCCCATGATGAGCAAAAGAAAAAAGCAACAGGCAGTAAATAAGTTGACAGAGATTGTCGCTAATTTTACCGCCATGATTTCTACCCGAATGCCtgatg                   <  2:730758/140‑1 (MQ=255)                                                                                                                                cGGTG‑AATTTTTTC‑AGACAAATAAAAAAAATGGAGGTGCCATGATGAGCGGAAGTAATAAAAAAAAAGCAGTGAATAAAATGAAAGAGATTGTCGCTAACTTTTCCCCCATGATTTTTACCCGAATGCCCGATGACgggg             >  2:669510/1‑140 (MQ=255)                                                                                                                                           ttCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                   >  2:185134/1‑124 (MQ=255)                                                                                                                                           ttCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCtgatg                   <  1:185134/124‑1 (MQ=255)                                                                                                                                            tCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTa  >  1:430296/1‑140 (MQ=255)                                                                                                                                             |                                                                                                                                            GCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACATTTTTAGTGGTAGTTTGTGGCGGTG‑AATTTTTCC‑AGACAAATACAAAAACTGGAGTTGCCATGATGAGCGAAAGTAATAAGCAACAGGCAGTGAATAAGTTGACAGAGATTGTCGCTAACTTTACCGCCATGATTTCTACCCGAATGCCTGATGACGTGGTGGATAAACTA  >  NC_000913/3206296‑3206573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑