Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,040,765	0	A	G	42.5%	49.7 / 14.1	40	intergenic (+129/+141)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
Reads supporting (aligned to +/- strand):  ref base A (19/4);  new base G (0/17);  total (19/21)
Fisher's exact test for biased strand distribution p-value = 6.94e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCG  >  NC_000913/4040617‑4040912                                                                                                                                                     |                                                                                                                                                     agTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑gg                                                                                                                                                   >  1:445384/1‑151 (MQ=31)      ggAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTTGGCCTTTCGTTTTATCTGTTGTTTGTCGGCGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGga‑gggagg                                                                                                                                               >  2:704173/1‑150 (MQ=9)       gAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCg                                                                                                                                             <  2:713625/151‑1 (MQ=31)          cTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGc                                                                                                                                          >  2:701273/1‑151 (MQ=31)            gCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGc                                                                                                                                          >  2:451012/1‑149 (MQ=31)              cAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAgg                                                                                                                                       >  1:16064/1‑150 (MQ=31)                ggCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGAc                                                                                                                                     <  1:286449/150‑1 (MQ=31)                  cATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGAcgcc                                                                                                                                  >  2:995214/1‑151 (MQ=31)                    tCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGAcgcccg                                                                                                                                >  2:779515/1‑151 (MQ=31)                       aaTAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGAcgcccgcc                                                                                                                              >  1:704650/1‑150 (MQ=31)                        aTAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                            >  2:842576/1‑151 (MQ=31)                                aagggCTCAGCGGGAAGCCTGGGCTTTTCTTTTTATTTGTTGTTTGTGGGTAAACCCTCTCTGGAGAAGGACAAACCCGCGGGGGGCGGATTTGAACGTTGCGAAGCAACGGCCGGGG‑GGGGGGGGGGCGGGCCGCCCGCCATAAACTg                                                                                                                      <  1:982922/146‑1 (MQ=2)                                      tCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCAt                                                                                                              >  1:189089/1‑151 (MQ=31)                                      tCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCAt                                                                                                              >  2:576555/1‑151 (MQ=31)                                            ggAAGACTGGGCTTTTCTTTTTTTGTTTTTTTTGTGGGGGACCCCCCTCTGGAGGAGAACAAACCCGCGGGGGGCGGTTTTCACGTTTGCAAAAAAACGGCCGGGA‑GGGGGGCGGGAAGGACCCCCGCCATAAACTGCCAGGCATCa                                                                                                            <  2:694989/147‑1 (MQ=2)                                                                                      cGCTCCCCGGAGTAGAACAAACCCGCGGGGAGCGGTTTTAAAGGTGGGGAAGAAACGGCCGGGG‑GGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgc                                                               <  2:444700/150‑1 (MQ=11)                                                                                          ctcCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgcgc                                                             >  1:551402/1‑148 (MQ=35)                                                                                            ccTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGaa                                                         >  1:731572/1‑150 (MQ=38)                                                                                                 gTAGAACAACTCCGCGGGGGGTGGATTTGAAGGTTGGGAAGCACCGGCCGGGG‑GGGTGGGGGGGGGGACTTCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGaa                                                         <  1:446651/145‑1 (MQ=14)                                                                                                   agaaaaaaCCCGCGGGGAGGGGATTTAAACTTTGCGAAGCAACGGCCGGGG‑GGGGGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATg                                                  <  2:862944/145‑1 (MQ=14)                                                                                                        aaccccgcggGGGGCGGTTTTAAACTTTGAGAAGAAACGGCGGGGG‑GGGTGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGAt                                            <  2:17659/147‑1 (MQ=17)                                                                                                        aaaTCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGAt                                            >  1:445341/1‑151 (MQ=255)                                                                                                        aaaTCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGAt                                            >  1:183472/1‑151 (MQ=255)                                                                                                        aaaCCCGCGGGGGGGGGTTTGGAACGTTGCGAAGCAACGGCCGGGG‑GGGGGGCGGGAAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATg                                                  <  1:28745/145‑1 (MQ=14)                                                                                                            ccgcggGGAGGGGTTTTGAATGTTGCGAAGAACCGGCCGGGG‑GGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGa                                        <  2:178943/151‑1 (MQ=17)                                                                                                            ccgcggGGAGGGGATTGGACCGTGGCGAAGAAACGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATg                                           <  2:101922/148‑1 (MQ=17)                                                                                                            ccgcggGGAGAGGATTTGAACTTTGGGAAGCAACGCCCGGGG‑GGGTGGGGGGAAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGa                                        <  2:496525/151‑1 (MQ=17)                                                                                                                 gggAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTg                                   >  2:846801/1‑151 (MQ=255)                                                                                                                  ggggCGGATTAGACGGTTGCAAAGCACCGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTgg                                  <  1:152797/148‑1 (MQ=18)                                                                                                                     ggggttttGAACGTTGCAAAGCAACGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGgcgc                               <  2:47047/146‑1 (MQ=18)                                                                                                                       ggttttGAACGTGGGAAAGCAACGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGcgcg                              <  2:16064/147‑1 (MQ=18)                                                                                                                          tttGAACTTTGCGAAGCACCGGCCGGGG‑GGGGGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGgcgc                               <  1:169213/146‑1 (MQ=255)                                                                                                                              aaggtggCGAAGCAGGGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATcc                      <  1:883657/145‑1 (MQ=18)                                                                                                                              aaCTTTGCGAAGCAGCGGCCGGGG‑GGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTAt                        <  1:842547/149‑1 (MQ=18)                                                                                                                                cGTTGCGAAGCAACGGCCCGGA‑GGGGGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATcc                      >  2:425673/1‑149 (MQ=255)                                                                                                                                    gCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCt                 >  2:766594/1‑150 (MQ=255)                                                                                                                                       aaGCAACGGCCGGGG‑GGGTGGGGGGAAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTAct              <  2:999610/150‑1 (MQ=255)                                                                                                                                        aGCAACGGGCGGGGGGGGTGGGGGGCGGGACCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCt                 <  1:153654/147‑1 (MQ=18)                                                                                                                                         gCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCtt           >  2:792795/1‑151 (MQ=255)                                                                                                                                              ggCCGGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCtt       <  2:802225/150‑1 (MQ=255)                                                                                                                                                  cGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCg  >  2:77978/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                     AGTAGGGAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGA‑GGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCG  >  NC_000913/4040617‑4040912

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑