Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,622,815	0	C	A	43.6%	49.3 / 22.5	41	intergenic (+74/+145)	yneM/dgcZ	inner membrane‑associated protein/diguanylate cyclase, zinc‑sensing
Reads supporting (aligned to +/- strand):  ref base C (21/1);  new base A (0/17);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 3.53e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGG  >  NC_000913/1622668‑1622956                                                                                                                                                         |                                                                                                                                              ttATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGa                                                                                                                                             >  1:209440/1‑150 (MQ=255)   aTGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGaaa                                                                                                                                           >  2:442209/1‑150 (MQ=255)        cGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAAc                                                                                                                                     >  1:240695/1‑151 (MQ=255)           aCTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGc                                                                                                                                  >  1:368182/1‑151 (MQ=255)              gggAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGcc                                                                                                                                 <  2:67186/149‑1 (MQ=255)                 aataatTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTa                                                                                                                             >  1:497933/1‑150 (MQ=255)                 aataatTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTa                                                                                                                             >  2:777478/1‑150 (MQ=255)                           ttttctggttttctggCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGt                                                                                                                   >  1:53609/1‑150 (MQ=255)                            ttcttgtttttcgggCCGCTTATTCCACCCA‑AAAGGGGATTGAAAAATGAAGGGAAAAAATCCCTC‑CCCAACCGGCCCCCTTGTT‑AAATTTGTCAAAAGGGGGGT‑TTTTTTTTAGG‑GAGGAAAAAAAAAACCGCCAGTAAACCGGCGGTg                                                                                                                  <  1:841361/143‑1 (MQ=255)                              tctggttttctggCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACcggcgg                                                                                                                    >  1:356835/1‑146 (MQ=255)                                tggttttctggCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAAt                                                                                                               >  1:680506/1‑149 (MQ=255)                                tggttttctggCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATg                                                                                                              >  1:781576/1‑150 (MQ=255)                                     ttctggCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGc                                                                                                         >  1:725607/1‑150 (MQ=255)                                           ccGCTTTTTCCACCCAAAAAGGGGA‑TAACAAAGGAAGGGAAATACCCCCCCCCCAACCCGC‑CCCTTTGTT‑ACAGTTGTGAAAAGGGGGCT‑TGTTTTTTAGG‑AGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATa                                                                                                  <  2:451222/151‑1 (MQ=255)                                             gcgTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGa                                                                                                    >  1:404116/1‑147 (MQ=255)                                             gcgTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                   >  2:781358/1‑148 (MQ=255)                                              cgTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAt                                                                                                   >  2:746654/1‑147 (MQ=255)                                                  tttCAGCAAAAAATGGAA‑TAACTAAAGAAAGGAGATAACCCCCCCCCTACCCGC‑CCCTTTTTT‑ACTTTTGTGAAAAGGGGTCT‑TTTTTTTTAGG‑CCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGAtt                                                                                              <  2:689698/148‑1 (MQ=255)                                                            aaaGGGGA‑TGACAAATAAACGGAAAAAACCCCCCCCCTCCCCGG‑CCCTTTTTT‑AAAGTTTGGAAAAGGGGGCG‑TGTTTTTTGGG‑ACGGGAAAAAAAGACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCtt                                                                                  <  2:865620/150‑1 (MQ=255)                                                            aaaGGGGA‑TAACAAATGAGGAGAAAAAACCCCTC‑CCCAACCCG‑CCCCTTTTTAACTTTTGTGAAAAGGGGGCT‑TTTTTTTTATG‑AGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCttt                                                                                 <  1:803137/151‑1 (MQ=255)                                                                gggA‑TGACAAAGGAAGGGAGATACCCCCTCCCCTACCCGC‑CCCTTTTTT‑AGAGTTGTGAACAGGGGGCT‑TGTTTTTTATG‑GGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTAc                                                                              <  2:54402/150‑1 (MQ=255)                                                                   gataaaaaaTGAACGGAAAAACCCCCCCCCCTACCCGC‑CCCTTTATA‑AGATTTGTGAACAAGGGCCC‑TGTTTTTTATG‑ACGAGAAAAAAAATCCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTa                                                                               <  1:715890/140‑1 (MQ=255)                                                                      gacaaagaaaggaagaAAATCCCTCCCCTACCCGT‑CTCCTTCTT‑AATGTTTTAAAAAGGGCGCT‑TTTTTTTTTGG‑ACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCt                                                                           <  2:284569/135‑1 (MQ=255)                                                                        cTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAAc                                                                        >  2:69560/1‑149 (MQ=255)                                                                          aaTGAGGGGAGATACCCCCCCACCTACCCGC‑CCCTTTTTT‑ACAGTTGTGTAAGGGGGGCT‑TGTTTTTTATG‑CGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACa                                                                       <  2:864978/148‑1 (MQ=255)                                                                                           ccTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGAt                                                    >  2:597916/1‑150 (MQ=255)                                                                                                  tAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATc                                            >  1:342104/1‑151 (MQ=255)                                                                                                  caaCCCG‑CCCTTTTTTAACATTTGTGTAC‑AGGGGCC‑TTTTTTTTAAGAACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAAt                                             <  2:725734/150‑1 (MQ=255)                                                                                                   acccGC‑CCCTTTTTT‑ACAGTTGTGTAAAGGGGGCT‑TGTTTTTTAGG‑ACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCg                                           <  2:1161/149‑1 (MQ=255)                                                                                                                 tt‑ACTGTTGTGAACAGGGGGCT‑TTTTTTTTAGG‑AGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAg                               <  2:677013/150‑1 (MQ=255)                                                                                                                          gtgtAAAGGGGGCT‑TGTTTTTAATG‑AGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGt                        <  1:527406/149‑1 (MQ=255)                                                                                                                              aCAGGGGGCT‑TTTTTTTTATG‑ACGAAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTTCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtctc                  <  1:110222/151‑1 (MQ=255)                                                                                                                                aaGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCa                 >  1:121529/1‑150 (MQ=255)                                                                                                                                 aGGGGCCGTGATTTTTATG‑ACGAAAAAAAAATACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAggt                       <  1:281167/144‑3 (MQ=255)                                                                                                                                  ggggCT‑TGTTTTTTATG‑CGGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTtc                    <  2:304591/145‑1 (MQ=255)                                                                                                                                         tGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGtt        >  1:628959/1‑151 (MQ=255)                                                                                                                                            tttttACG‑CCGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaa      <  2:107816/150‑1 (MQ=255)                                                                                                                                             ttttATG‑ACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTaaa     <  2:781713/150‑1 (MQ=255)                                                                                                                                               ttATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGAGAGATTTGTGGTTTGCTTTTACGCTAACAGGCATTTTCCTACACTGATAAAGAATCGGTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg  >  2:502780/1‑151 (MQ=255)                                                                                                                                                tATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg  >  2:528445/1‑150 (MQ=255)                                                                                                                                                   g‑ACGGAAAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACgg  <  1:344319/147‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                              TTATGGCCGTACTGGGAATAATTTTATTTTCTGGTTTTCTGGCCGCGTATTTCAGCCACAAATGGGA‑TGACTAATGAACGGAGATAATCCCTCACCTAACCGG‑CCCCTTGTT‑ACAGTTGTGTACAAGGGGCC‑TGATTTTTATG‑ACGGCGAAAAAAAACCGCCAGTAAACCGGCGGTGAATGCTTGCATGGATAGATTTGTGTTTTGCTTTTACGCTAACAGGCATTTTCCTGCACTGATAACGAATCGTTGACACAGTAGCATCAGTTTTCTCAATGAATGTTAAACGG  >  NC_000913/1622668‑1622956

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: ‑