Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,412,898	0	C	T	45.1%	36.8 / 45.8	52	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (21/7);  new base T (0/23);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 1.08e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTC  >  NC_000913/3412748‑3413042                                                                                                                                                       |                                                                                                                                                 aTCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGc                                                                                                                                                  >  2:943327/1‑151 (MQ=255)   ccACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCtt                                                                                                                                                <  1:614896/151‑1 (MQ=255)   ccACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCtt                                                                                                                                                <  1:591988/151‑1 (MQ=255)        aaaaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                            <  1:129115/150‑1 (MQ=255)        aaaaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                            >  1:578460/1‑150 (MQ=255)           aCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                        <  2:404511/151‑1 (MQ=255)              ggTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                        >  1:854674/1‑148 (MQ=255)                   aCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATa                                                                                                                                <  2:560905/151‑1 (MQ=255)                        gACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAAccc                                                                                                                            <  1:402607/150‑1 (MQ=255)                             aCTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCat                                                                                                                       >  1:779370/1‑150 (MQ=255)                                    tttCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCAtt                                                                                                                >  1:525632/1‑150 (MQ=255)                                     ttCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTa                                                                                                               >  1:322625/1‑150 (MQ=255)                                        aGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAAcc                                                                                                            >  2:712274/1‑150 (MQ=255)                                             aaaaTGTGATTTTAAATGACTTTTAATTTATTCGTTTGATAAATTAATTTCTTTATTTTTTCATCTGGAATAAACTTTCTTAATCCTTTATCGCCAAGAGGGGGGGTTTTTTTATAAAAATAAAAACCCGCCATATTCATTAACCAGttt                                                                                                       <  1:805599/148‑1 (MQ=255)                                                 tgtgAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAAc                                                                                                  >  1:501800/1‑151 (MQ=255)                                                       tttACTTGCCCCTTAATTCTTTCTTTTGATGAATTAATTTCTTTATTTTTTCATCTGCCATAAACATTTTAAATTCTTTATCGACAAGGGGGGGGGTTTTTTTAAAAAGCTAATACCCCGCCATATTCATTAACCAGTTTTGAACAAtt                                                                                              <  1:434668/149‑1 (MQ=255)                                                       tttACATGACATTTAATTCATTCTTTTGATAAATTATTTTCTTTTTGTTTTCTTCTGGCATAAACATTCTTAATACTTTATCGACCAGAGGGGGGGTTTTTTTATAAAAATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAAt                                                                                               <  1:585635/148‑1 (MQ=255)                                                        ttACATGACATTTAATTCTTTTTTTTGATAAATTATTTTTTTTTTTTTTTCATCTGGCATAAACTTTTTTAATCCTTTACCGCCCAGGGGGGGGGTTTTTTTATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTcc                                                                                            <  1:141975/150‑1 (MQ=255)                                                               aaacTTAATTCATTCGTTTGATGAATTAATTTTGTTTTATTTTCATCTGGCATAAACATTTTTTATAATATATTGAACAAAGCGGGGGGTTGTTTTTAAAGATCATAAACCGCCATATTCATTTAACAGATTTTAACAATTTCGCTgta                                                                                      >  2:274467/3‑147 (MQ=255)                                                                   ttAATTTTTTCGTTTGATAAATTATTTTCTTTATTTTTTCATTTGGCATAAACATTTTTAATCCTTTATCGACAGGAGGGGGGTTTTTTTTAAAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCAc                                                                                 <  1:553310/150‑1 (MQ=255)                                                                   ttAATTCTTTCTTTTGATAAATTATTTTCTTTATTTTTTCATCTGACATAAACATTCTTAATATTTTATCGCCGAGAGCGGGGTTTTGTTTATAAAAAACAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCa                                                                                  <  1:597545/149‑1 (MQ=255)                                                                   ttAATTCTTTCTTTTGATAAATTAATTTCTTTTTTTTTTCATCTGGCATAAACTTTCTAAATACGTTATCGCCAAGGGGGGGGGTTTTTTTAAAAAGATAAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAg                                                                                     <  1:449653/146‑1 (MQ=255)                                                                       ttctttctTTTGATAATTTATTTTTTTTATTTTTTATTCTGGCATAAACATTTTTAATACTTTATCGCCCAGGGGGGGGTTTTGTTAAAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCa                                                                               <  2:428822/148‑1 (MQ=255)                                                                            tcttttGATGAATTAATTTCTTTTTTTTTTCATCTGGAATAAACTTTCTTAATACGTTATCGACCAGGGGGGGGGTTTTTTAATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataa                                                                        <  2:108006/147‑1 (MQ=255)                                                                            tcGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataat                                                                       >  2:111232/1‑151 (MQ=255)                                                                                   atgaATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatcatc                                                                >  2:161611/1‑151 (MQ=255)                                                                                              tttttttGTTTTCTTCTGGAATAAACTTTATTAATCCTTTATCGACGAGGGCGGGGTTTTTTTAATAAAAATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTa                                                      <  2:558174/144‑1 (MQ=255)                                                                                               cGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaa                                                     >  2:245201/1‑150 (MQ=255)                                                                                               cGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaa                                                     >  2:457184/1‑150 (MQ=255)                                                                                                gTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAAt                                                   >  2:85601/1‑151 (MQ=255)                                                                                                  tATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCg                                                 >  1:872074/1‑151 (MQ=255)                                                                                                     gTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAgg                                              >  1:128308/1‑151 (MQ=255)                                                                                                      ttttCTTCTGGAATAAACTTTCTAAATCCTTAATGACCCAGAGCGGGGGTTTTTTAATAAAAATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCg                                                 <  2:400089/147‑1 (MQ=255)                                                                                                         tCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAt                                          >  2:573312/1‑151 (MQ=255)                                                                                                               ggaataaaCTTTCTTAATACGTTATCGCCAAGGGGGGGGGTTTGTTAAAAAAGATAAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAttt                                        <  2:270369/141‑1 (MQ=255)                                                                                                               ggaataaaCATTTTAAATCCTTTACCGACCGGGGGGGGGTTTTTTTTAAAAAGATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGc                                      <  1:521278/143‑1 (MQ=255)                                                                                                               ggCATAAACATTTTTAATACGTTACCGACAAGGGGGGGGGTTTGTTTATAAAGACAAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTg                                       <  1:743721/148‑1 (MQ=255)                                                                                                                 cATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTac                                   >  2:903550/1‑150 (MQ=255)                                                                                                                  ataaatttttttAATTCTTTACCGACAGGGGGGGGGTTTTTTTTAAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTacac                                 <  2:976943/141‑1 (MQ=255)                                                                                                                    aaaCTTTTTTAATCCTTTATCGCCCAGGGCGGGGTTTTGTTTAAAAAAATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTaca                                  <  2:684518/147‑1 (MQ=255)                                                                                                                     aaCATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTATACAAc                              >  1:671090/1‑151 (MQ=255)                                                                                                                         ttcttatgtctttATCCACCAGAGGGGGGTTTTTTTAAAAAAGACAAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAAcc                             <  2:929824/137‑1 (MQ=255)                                                                                                                            ttAATCCTTTATCGACCAGGGGGGGGGTTTTTTTATAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCttgtt                        <  1:859239/150‑1 (MQ=255)                                                                                                                              aatcttttatgctccAGGGCGGGGGCTTTTTTAAAAAGATCAGACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCttgttg                       <  1:87359/136‑1 (MQ=255)                                                                                                                              aaTACTTTATCGACCAGAGGGGGGTTTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCttgttg                       <  1:349172/149‑1 (MQ=255)                                                                                                                                tACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                    >  2:254137/1‑150 (MQ=255)                                                                                                                                  cGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGac                  >  1:97816/1‑150 (MQ=255)                                                                                                                                  cGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGac                  >  1:534414/1‑150 (MQ=255)                                                                                                                                    ttATCCACCAGAGGGGGGGTTTTTTTAAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGacac                <  1:688731/150‑1 (MQ=255)                                                                                                                                        cGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTg           >  2:972538/1‑151 (MQ=255)                                                                                                                                           cgagggggggggTTTTTTTAAAAAGAAAAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGc              <  2:549961/138‑1 (MQ=255)                                                                                                                                                  gggggTTTTTTTAAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTc  <  1:407163/150‑1 (MQ=255)                                                                                                                                                  gggggTTTTTTTAAAAAGATAATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTc  <  1:816562/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                 ATCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTCATCTGGCATGAACATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTTC  >  NC_000913/3412748‑3413042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑