Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,292,458	0	T	A	41.2%	72.5 / 25.1	51	intergenic (+93/+51)	galU/hns	glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
Reads supporting (aligned to +/- strand):  ref base T (25/5);  new base A (0/21);  total (25/26)
Fisher's exact test for biased strand distribution p-value = 6.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCTTGGCACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTCCAGGTTTT  >  NC_000913/1292311‑1292604                                                                                                                                                    |                                                                                                                                                   ccTTGGCACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATaaa                                                                                                                                                 <  2:179243/151‑1 (MQ=255)   ttGGCACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAAAATCCGTATCGGTGTTATCAACGAAACGGCGTTGTGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACGGGAAAATaaaa                                                                                                                                                >  2:320879/1‑150 (MQ=255)    tGGCACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATaaaaa                                                                                                                                               >  2:82334/1‑150 (MQ=255)       cACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATcc                                                                                                                                           <  2:198445/151‑1 (MQ=255)           gAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCccgcc                                                                                                                                       <  2:902238/151‑1 (MQ=255)               ttAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCt                                                                                                                                    >  2:758326/1‑150 (MQ=255)                tAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTgg                                                                                                                                  >  1:635181/1‑151 (MQ=255)                   aGCCTGTCTTGAAGAAGAGATGGGCATTAAGAATTAACACCCGTATCGTTTTTATCCACAAAACGGCGTTGAGCAATCGACGCCTTTTTTTTATAGCTTATTCTTATTAAATTGTCTAAACCCGAACAAAAAAAAATCCCGCCGCTgg                                                                                                                                  <  2:51688/148‑1 (MQ=255)                     ccgggCTTAAAAAAAAGAGGGGTATTAAAAAGTAACACCCGTTTGGGTGTTACCCACAAAACGGGGTTGAGAAACCGACGCCGTTTTTTTATAGCTTATTTTTATTAAATTTTTTAAACCCGGACAAAAAAAACTCCCGCCGCTGGCGGGa                                                                                                                             <  2:641061/148‑1 (MQ=255)                     ccTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCggg                                                                                                                              >  2:971413/1‑150 (MQ=255)                      cTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGa                                                                                                                             >  2:950369/1‑150 (MQ=255)                         gCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGAtttt                                                                                                                         >  1:636083/1‑151 (MQ=255)                              aaaaagaGATGGGCATAAAGAAGAAACATCCTTATCGGTGTTATCCACGAAACGGCGTTGAGAAATCGACGCCGTTTTTTTATAGTTTATTCTTATTAAATTGTCTTAACCCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAg                                                                                                                      <  1:153234/146‑1 (MQ=255)                                 aagaGATGGGCATTAAGAAGTAACATCGTTTTCGGTTTTATCCACGAAACGGCGTTGAGCAATCGACGCCTTTTTTTTATAGCTTATTCTTATTAAATTGTTTAAAACCGAAAAAAAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGt                                                                                                                 <  2:139900/151‑1 (MQ=255)                                     gaTGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACTAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCa                                                                                                              >  2:338488/1‑150 (MQ=255)                                      aTGGGCATTAAAAATTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAACCGACGCTTTTTTTTTATAGCTTATTCTTATAAATTTGTCTAAAACCGGACAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGc                                                                                                               <  2:617973/148‑1 (MQ=255)                                        gggCATAAAGAATAAACCTCCGTTTCGGTGTTACCCACGAAACGGCGTGGAGCAATCGCCGCGGTTTTTTTATAGTTTATTCTTATAAATTTTTCTTAACCCGAAAAAAAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAAt                                                                                                            <  2:83123/149‑1 (MQ=255)                                        gggCATAAAGAAGTAACATCCGTATGGGTTTTATCCACGAAACGGTTTTGAGAAATCGACGCGTTTTTTTTATAGCTTATTCTTATAAATTTTTCTTAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATc                                                                                                           <  2:45150/150‑1 (MQ=255)                                            ataaagaagTAACATCCGTATCGGTTTTACCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTAAAACCGGACAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTAc                                                                                                        <  1:937942/146‑1 (MQ=255)                                            aTTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACa                                                                                                       >  2:756852/1‑150 (MQ=255)                                               aagaagTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACaaa                                                                                                     >  1:379503/1‑149 (MQ=255)                                                     tAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGattatt                                                                                             >  2:275548/1‑151 (MQ=255)                                                          tCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCtt                                                                                         >  1:669273/1‑150 (MQ=255)                                                               aTCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCTTTTTTTTTATAGCTTATTTTTATTAATTTGTCTAAAACCGAAAAAAAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCa                                                                                    <  2:425664/150‑1 (MQ=255)                                                               aTCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATc                                                                                     >  2:261985/1‑149 (MQ=255)                                                                    tgtttcccACGAAACGGCTTGAAGCAACCGACGCGTTTTTTTTATAGTTTATTCTTTTTAAATTTTCTTAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGaaa                                                                               <  1:885194/144‑1 (MQ=255)                                                                    tgtTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAAt                                                                              >  1:408429/1‑151 (MQ=255)                                                                         tCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAAtcgtcg                                                                         >  1:52040/1‑151 (MQ=255)                                                                               aaaGGGGGTTGACCATCCGACCCTTTTTTTTTATGGTTTATTCTTATTAATTTGTCTCAAACCGAAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAgg                                                                      <  1:683353/148‑1 (MQ=255)                                                                                aaCGGCGTTGAGCAATCGACGCCTTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGAAAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGAtt                                                                  <  1:45753/151‑1 (MQ=255)                                                                                          aGCAATCGGCGCCGTTTTTTTATAGCTTATTTTTATTAAATTGTCTTAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTg                                                           <  2:15006/148‑1 (MQ=255)                                                                                             aaTCGACGCTTTTTTTTTATAGCTTATTTTTATTAATTTGTTTAAACCCGAAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTc                                                        <  2:274209/148‑1 (MQ=255)                                                                                                    gCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCt                                              >  2:16610/1‑151 (MQ=255)                                                                                                         ttttttAGATTTTATTCTTTTAAAATTGTCTTAACCCGGATAATAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCttttt                                          <  1:901159/150‑1 (MQ=255)                                                                                                           ttttATAGCTTATTCTTATTAAATTGTCTTAAACCGAAAAAAAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTg                                        <  1:496996/150‑1 (MQ=255)                                                                                                            tttATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGAt                                      >  2:876977/1‑151 (MQ=255)                                                                                                             ttATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGAtt                                     >  2:101556/1‑151 (MQ=255)                                                                                                               ataGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTa                                    >  2:907158/1‑150 (MQ=255)                                                                                                                        tcttattAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGt                          >  2:91750/1‑151 (MQ=255)                                                                                                                        tcttattAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGt                          >  1:534930/1‑151 (MQ=255)                                                                                                                        tcttattAAATTGTCTAAAACCGGAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAg                           <  2:94488/150‑1 (MQ=255)                                                                                                                          ttataaAATTGTCTTAAACCGGACAAAAAAAAACCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTa                         <  1:124788/150‑1 (MQ=255)                                                                                                                               aaaTTGTCTTAAACCGGACAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCt                   <  1:264012/151‑1 (MQ=255)                                                                                                                                aaTTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCtt                  >  1:80184/1‑151 (MQ=255)                                                                                                                                      cTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGcc              >  2:337198/1‑149 (MQ=255)                                                                                                                                         aaaCCGAAAAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGc               <  1:472129/145‑1 (MQ=255)                                                                                                                                           aCCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTcc         >  1:1043254/1‑149 (MQ=255)                                                                                                                                              ggAAAAAAAAAAGCCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTCCAGGt     <  1:655067/150‑1 (MQ=255)                                                                                                                                               aaCAAAAAAAAAGCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTCCAGGttt   <  2:632137/150‑1 (MQ=255)                                                                                                                                                aCAATAAAAAATCCCGCCGCTGGCGGGACTTTAAGCTAGTGCAATCTACAAAAATTTATTGCTTGATCAGGAACTCCCCGAGTGATTTACCCATCTCATCCATTGCTTTTTTGATTACAGTTGGAGTACGGTCTTGGACAGTCCCGTtttt  >  2:123627/1‑151 (MQ=255)                                                                                                                                                aCAAAAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTCCAGGtttt  <  1:1003667/151‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                   CCTTGGCACGGAATTTAAAGCCTGGCTTGAAGAAGAGATGGGCATTAAGAAGTAACATCCGTATCGGTGTTATCCACGAAACGGCGTTGAGCAATCGACGCCGTTTTTTTATAGCTTATTCTTATTAAATTGTCTTAAACCGGACAATAAAAAATCCCGCCGCTGGCGGGATTTTAAGCAAGTGCAATCTACAAAAGATTATTGCTTGATCAGGAAATCGTCGAGGGATTTACCTTGCTCATCCATTGCTTTTTTGATTACAGCTGGAGTACGGCCTTGGCCAGTCCAGGTTTT  >  NC_000913/1292311‑1292604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑