Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,163	0	C	T	44.9%	53.6 / 24.6	49	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (4/23);  new base T (22/0);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 4.34e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

TTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGG  >  NC_000913/1487018‑1487313                                                                                                                                                   |                                                                                                                                                         tttATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTtcctcc                                                                                                                                                      <  1:332178/150‑1 (MQ=255)    attaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCttt                                                                                                                                                   <  2:645909/150‑1 (MQ=255)            tAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACAAACAA‑ATTTCTCCtttt                                                                                                                                                  >  1:580552/1‑142 (MQ=255)              aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAAAGA‑ATTTTTCCtttttta                                                                                                                                               >  2:951550/1‑140 (MQ=255)                 cGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAATGAAAAAAAA‑TTTTCTCCttttttagtggtcccc                                                                                                                                      >  2:400315/1‑137 (MQ=255)                           aaaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGTTAAGAAAAAAAA‑TTTTCTCCCTTTAGAGTGCTCCGCTTCTCACtatt                                                                                                                           >  1:870254/1‑151 (MQ=255)                            aaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAAGA‑ATTTCTCCTTTCATAGTGGTTCGcct                                                                                                                                    >  1:584286/1‑139 (MQ=255)                                  cAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCAc                                                                                                                    <  1:978191/151‑1 (MQ=255)                                         tCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTa                                                                                                              <  1:179308/150‑1 (MQ=255)                                          cAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGAACATAAAA‑ATTTCTCCTTTCTTAGTGCTTCCCCTCTCACTATTATTTCACCCAGTA‑tt                                                                                                           >  2:332449/1‑151 (MQ=255)                                          cAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATATCAGGCTTGCGGAGTGGCGGTTAAGGAAATAAGA‑TTTTCTCCCTTCTGAGTGCTCCCCCTCTCCCTATTTTTTCACCCAGTA‑tt                                                                                                           >  1:775962/1‑151 (MQ=255)                                           aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAAAAA‑TTTTCTCCTTTTAGAGGGGTCCGCCTCTCACTATTTTTTCACCCAGTA‑tt                                                                                                           >  1:288102/1‑150 (MQ=255)                                                aaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAATAAGA‑ATTTCTCCTTTCTTAGTGCTCCGCTTCTCCCTATTATTTCACCCCGTA‑Tttttta                                                                                                      >  2:953945/1‑148 (MQ=255)                                                  tACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAAAAAGA‑TTTTCTCCTTTTCGAGTGCTCCGCTTCTCCCTATTTTTTTACGCCGGA‑Ttttttaagg                                                                                                   >  1:88182/1‑146 (MQ=255)                                                      aTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAGA‑ATTTCTCCTTTTAGAGTGGTCCGCTTCTCTCTATTATTTTCCGCAGGA‑TTTTTTAAGGaa                                                                                                 >  1:655208/1‑149 (MQ=255)                                                        tctcTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGa                                                                                              <  1:99102/150‑1 (MQ=255)                                                           ctgctgCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGTAAGGACATAAGA‑TTTTCTTCCTTCACCAGGCTCCGCCTCTCCCCATTTTTTCACCCAGCA‑TTCTTTATGGGAAGATaa                                                                                           >  2:592480/1‑150 (MQ=255)                                                             gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAagga                                                                                        <  2:1014740/151‑1 (MQ=255)                                                                gcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAggagga                                                                                     <  1:510595/151‑1 (MQ=255)                                                                 cAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGaa                                                                                    <  1:525705/151‑1 (MQ=255)                                                                   aGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAATAAAA‑TATTCTCCTTTCTTAGGGGGCCGCCTCTCACTATTTTTTCACGCAGGA‑TTTTTTAAGGAACGATAAAGAGGGAcc                                                                                  >  2:349740/1‑151 (MQ=255)                                                                    gATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCa                                                                                 <  2:234789/151‑1 (MQ=255)                                                                     aTGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGGAAAGACATAAGA‑ATTTCTCCTTTTTGAGGGGGCCGCTTTTCCCCATTCTTTTACGCAGGATTTTTTAAGGGGACG‑TAaggagg                                                                                      >  2:644961/1‑145 (MQ=255)                                                                        aataatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGa                                                                              <  2:365141/150‑1 (MQ=255)                                                                         ataatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGACATAAAA‑TATTCTCCTTTTTTAGGGCTCCCCCTTTCCCTATTATTTTCCGCAGAA‑TTTTTTTGGGGACGATAAAGAGGAAACAAGaa                                                                             >  2:918265/1‑150 (MQ=255)                                                                          taatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACATAAGA‑ATTTCTCCTTTTTGAGGGCTCCGCCTCTCCCTATTTTTTTACCCCGGATTTTTTTAGGGAA‑GATAAAGAGGAAACaataa                                                                             >  2:810008/1‑145 (MQ=255)                                                                          taatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACAAAATATTTTCCCCCTTTC‑TAGGGCGCCGCTTCTTCCTATTATCTCACGCCGCC‑TTCTTTAAGGAACGATAAGGGGGGAACATCaa                                                                             >  1:747118/1‑149 (MQ=255)                                                                                      aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCg                                                                  <  2:511092/147‑1 (MQ=255)                                                                                      aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTc                                                              <  2:511630/151‑1 (MQ=255)                                                                                      aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTc                                                              <  2:925780/151‑1 (MQ=255)                                                                                       cAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAACA‑TTTTCTCCTTTTCGAGTGCTCCCCTTCTCCCTTTTTTTTCACCCCGTA‑TTTTTTAGGGGACGATAAAGGGGAAACATGAACATTT‑CCCCCttttc                                                             >  1:496209/1‑149 (MQ=255)                                                                                         gCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACGA‑TTTTCTCCTTTTTGAGTGGCCCCCCTTTCCCTTTTATCTCACCCCGGA‑TTTTTTAAGGAAAGATAAAGAGGAAACATGAAAATTA‑CCCCCttttc                                                             >  1:645979/1‑147 (MQ=255)                                                                                            tttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAGA‑TTTTCTCCTTTTTGAGTGCTCCGCCTCTCCCTATTTTTTCCCCCCGTA‑TTTTTTAAGGAACGATAAAGAGGGACCAAGAACAATA‑CCCCCTTTTCGACGc                                                        >  1:857233/1‑151 (MQ=255)                                                                                            tttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAAAAAAA‑ATTCCTCCTTTTAGAGGGCGCCCCCTCTCTCTATTATTTCACGCAGTA‑TTTTTAAAGGAAAGATAAAGAGGAAACATGAAAAATT‑CCCCCTTTccgccg                                                         >  1:249004/1‑150 (MQ=255)                                                                                             ttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACAAACGA‑TTTTCTCCTTTTTGAGGGCTCCCCCTCTCCCTATTATTTCACCCCGTATTTTTTAAGGGAA‑GATAAAGAGGAAACATGAAAAATATCCCCCTTTccccgc                                                         >  1:273157/1‑146 (MQ=255)                                                                                             ttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGc                                                        <  2:731593/150‑1 (MQ=255)                                                                                               ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAACGA‑TTTTCTCCCTTTTAAGGGCTCCCCCTCTCACCAATTTCTCCCCCCGGA‑TTTTTAATGGGAAGAAAAAGAGGAAACACAAACAATA‑ACCCCCTTCCGCCGCctt                                                     >  1:889469/1‑151 (MQ=255)                                                                                                  tAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTc                                                    <  2:826399/149‑1 (MQ=255)                                                                                                   aaaaGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGc                                                  <  2:273141/150‑1 (MQ=255)                                                                                                    aaaGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCg                                                <  2:47985/151‑1 (MQ=255)                                                                                                     aaGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACCA‑TTTTCTCCTTTCAGAGGGCTCCGCTTCTCACTATTATCTCACCCAGTA‑TTCTTAAGGGGACGATAAGGAGGAAACATGAACATTA‑CCCCGCTTCCGCCGCCTTCGCCgg                                               >  2:681469/1‑151 (MQ=255)                                                                                                              cAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAg                                      <  2:567737/151‑1 (MQ=255)                                                                                                                ggCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGAt                                    <  1:486942/151‑1 (MQ=255)                                                                                                                     gCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCAt                               <  2:679304/151‑1 (MQ=255)                                                                                                                      cGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATa                              <  1:822699/151‑1 (MQ=255)                                                                                                                      cGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATa                              <  1:444202/151‑1 (MQ=255)                                                                                                                          gTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATg                          <  2:581623/151‑1 (MQ=255)                                                                                                                                 ttAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCgg                   >  2:495601/1‑151 (MQ=255)                                                                                                                                  tAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCgg                   >  2:148735/1‑150 (MQ=255)                                                                                                                                    aGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACa                <  1:968883/151‑1 (MQ=255)                                                                                                                                                   cctcctTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAgg  <  1:470844/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                         TTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACATACGA‑TTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTAAGGGAACGATAAGGAGGAACCATGAACATTA‑CCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGG  >  NC_000913/1487018‑1487313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑