Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,153	0	C	A	43.8%	99.5 / 22.8	48	intergenic (+190/‑82)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (3/24);  new base A (21/0);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.81e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAC  >  NC_000913/1487012‑1487298                                                                                                                                               |                                                                                                                                                      gggTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAATaaaatt                                                                                                                                               >  2:793869/1‑145 (MQ=255)               ttCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATAcaaatt                                                                                                                                              >  2:938952/1‑132 (MQ=255)                tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGt                                                                                                                                <  1:529248/150‑1 (MQ=255)                tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGt                                                                                                                                <  1:47048/150‑1 (MQ=255)                tCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAAAAATTTTTTCCtttttcagtg                                                                                                                               >  2:270009/1‑144 (MQ=255)                    aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAAAAAAAATTTCTCCTTTCTGAGTGCTcc                                                                                                                           >  1:79673/1‑151 (MQ=255)                    aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAACGATTTTCTCCTTTTAGAGTGCTcc                                                                                                                           >  1:410107/1‑151 (MQ=255)                       cGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑t                                                                                                                       <  2:701456/151‑1 (MQ=255)                           aaGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑GTTAAGAAATAAGAATTTCTCCttttcaaggggtc                                                                                                                            >  2:200001/1‑133 (MQ=255)                             gggTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCAc                                                                                                                 <  1:140581/151‑1 (MQ=255)                             gggTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑ATAAAGAAAAAACAATTTCTCCTTTTTGAGGGCTCCCC‑Ttcttcc                                                                                                                 >  2:132376/1‑148 (MQ=255)                                   aaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATAAGAATTTCTCCTTTTTGAGTGCTCCGC‑CTCTCACtattat                                                                                                           >  2:274970/1‑151 (MQ=255)                                     aTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTAtct                                                                                                         <  2:86883/151‑1 (MQ=255)                                      ttCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATACGATTTTTTTCCTTTTTAGTGGTCCCC‑CTCTCTCtattattt                                                                                                         >  2:603952/1‑148 (MQ=255)                                           gAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCa                                                                                                   <  2:351805/151‑1 (MQ=255)                                           gAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCa                                                                                                   <  1:892371/151‑1 (MQ=255)                                            aaTTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑g                                                                                                 <  1:465047/151‑1 (MQ=255)                                               tCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTa                                                                                               <  1:313593/150‑1 (MQ=255)                                               tCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTa                                                                                               <  2:240896/150‑1 (MQ=255)                                                cAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAAAACAATCTTCCCCTTTTAGAGGGCGTCGC‑TTCTTAATATCATTTCTCGctg                                                                                                  >  2:828256/1‑145 (MQ=255)                                                cAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTAtt                                                                                             <  2:178419/151‑1 (MQ=255)                                                 aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTc                                                                                            <  2:171409/151‑1 (MQ=255)                                                 aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAACAAATTTCTCCCTTTAGAGGGGTCCCC‑TTCTCACTATTTTTTCACGCA‑gg                                                                                                >  1:356396/1‑146 (MQ=255)                                                   aaaaaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATACAAATTTTTCCTTTTTGAGTGTGCCGC‑TTTTCACTATTAtttcccccaagattttt                                                                                           >  2:999667/1‑138 (MQ=255)                                                          cAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGaa                                                                                  <  2:790959/151‑1 (MQ=255)                                                                   gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAag                                                                          <  2:251762/149‑1 (MQ=255)                                                                   gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAACGATTTTCTTCTTTTCGAGTGCTCCCC‑TTCTCACTATTTTTTCACGCC‑GTATTC‑TTTAAGGAAAG‑ATaa                                                                           >  1:529200/1‑148 (MQ=255)                                                                    ctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAACAAATTTCTCCCTTTCGAGTGCTCCCC‑CTCTCACTATTATTTCACCCA‑GGATTC‑TTAAAGGAAAG‑ATaa                                                                           >  1:182728/1‑147 (MQ=255)                                                                     tgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAAAGAATTTCTCCTTTTTGAGGGGTCCCC‑TTTTCACTATTTTTTTCCGCA‑GGATTCTTTAAGGGAA‑G‑ATaa                                                                           >  1:651568/1‑146 (MQ=255)                                                                       cAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGaa                                                                    <  1:808193/151‑1 (MQ=255)                                                                          gATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCa                                                                 <  1:663115/151‑1 (MQ=255)                                                                              aataatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCGCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGa                                                              <  1:258871/150‑1 (MQ=255)                                                                                 aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGCTTCAGAAATAACAATTTCTTCCTTTC‑GAGTGGCCCGCGTTTTCCCT‑TTTTTTTACGCA‑GGATTC‑TTTTGGGGAAG‑AAAaagagggaacaataaaa                                                           >  2:484254/1‑139 (MQ=255)                                                                                 aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACa                                                           <  1:39725/150‑1 (MQ=255)                                                                                    gTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTa                                                        <  2:333919/150‑1 (MQ=255)                                                                                            aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTc                                               <  1:249773/151‑1 (MQ=255)                                                                                             cAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAACGAATTTCTCCTTTTAGAAGGGTCCGC‑TTCTCTCTATTTTTTCACGCA‑GTATTT‑TTTAGGGGACG‑AAAAAGAGGAACCATAAACAATAcccccctt                                                >  2:116465/1‑145 (MQ=255)                                                                                                     ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCttt                                      <  2:87904/151‑1 (MQ=255)                                                                                                     ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATAAAATTTTCTCCTTTTAGAGGGGTCCGC‑TTTTCACTATTTTCTCACCCAGGTTTTT‑TTAAGGGAA‑G‑ATAAAGAGGAAACATGGACATTACCCCGTTTTCGACGCttt                                      >  1:416346/1‑151 (MQ=255)                                                                                                         aaaaGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAAAAAGATTTTCTCCCTTTAAAATGCTTCCC‑CTCTCACTATTATTTCACGCA‑GGATTT‑TTTATGGGAAG‑AAAAAGAGGGAACACGAAAAATACCCCCTTTCCCACGCTTTCGcc                                  >  1:187687/1‑151 (MQ=255)                                                                                                           aaGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAATACAATTTTCTCCTTTTTGAGGGCTCCGC‑CTCTCACTATTTTTTTCCGCA‑GGATTT‑TTTAGGGGACG‑AGAAAGAGGGAACATGAAAATTAACCCCTTTTCGCCGCTTTTGCCgg                                >  1:210697/1‑151 (MQ=255)                                                                                                            aGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAATAAGAATTTCTCCTTTTCGAGTGGCCCCC‑CTCTCCCCATTTTTTCACACA‑GTATTT‑TTTAGGGAAAGAAAAAGGGGGAACC‑TTAACAATACCCCCCTTTCCACGCCTTTGcccg                                >  2:393258/1‑148 (MQ=255)                                                                                                                  gTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACtat                         <  2:511400/151‑1 (MQ=255)                                                                                                                       gCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATg                    <  1:247074/151‑1 (MQ=255)                                                                                                                                 tGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGt          >  2:679405/1‑151 (MQ=255)                                                                                                                                          aaGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGa   <  2:153773/150‑1 (MQ=255)                                                                                                                                          aaGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAc  >  1:754540/1‑151 (MQ=255)                                                                                                                                           aGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAc  >  1:981578/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                      GGGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGC‑TTCTCACTATTATCTCACGCA‑GTATTC‑TTAAGGGAACG‑ATAAGGAGGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAC  >  NC_000913/1487012‑1487298

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑