Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,040,772	0	C	G	42.5%	47.3 / 12.6	40	intergenic (+136/+134)	rrfA/mobB	5S ribosomal RNA of rrnA operon/molybdopterin‑guanine dinucleotide biosynthesis protein B
Reads supporting (aligned to +/- strand):  ref base C (15/8);  new base G (0/17);  total (15/25)
Fisher's exact test for biased strand distribution p-value = 1.26e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTT  >  NC_000913/4040623‑4040921                                                                                                                                                      |                                                                                                                                                      gAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCg                                                                                                                                                      <  2:263009/151‑1 (MQ=31) gAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCg                                                                                                                                                      <  1:697198/151‑1 (MQ=31)   aCTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGTGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCgg                                                                                                                                                     <  1:247218/150‑1 (MQ=14)          ggCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcg                                                                                                                                             >  2:673241/1‑151 (MQ=31)            cATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcgcc                                                                                                                                           <  2:798857/151‑1 (MQ=31)                aaaTAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAcgcccgcc                                                                                                                                       <  1:132358/151‑1 (MQ=31)                  aTAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCAt                                                                                                                                     >  1:814467/1‑151 (MQ=31)                      aaCGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATaaa                                                                                                                                  >  2:701830/1‑150 (MQ=31)                                 cAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATc                                                                                                                      >  1:762566/1‑151 (MQ=31)                                      ggAAGACTGGGCTTTTCTTTTTATCTGTTTTTTGTGGGTGAACGCTCTCATGAGTGGGACAACCCGGCGGGGGGCGGTTTTGACGGTTGCGAAGCACCGGCCGGGGGGGGGGGGGGCAGGGCGCCCGCCATAAACTGCCAGGCATCaa                                                                                                                    <  2:633691/148‑1 (MQ=2)                                       gAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAAtt                                                                                                                 >  2:840275/1‑150 (MQ=11)                                                                          ggTGACCGCTCTCCGGAGTAGGAAAAACCCGCGGGGGGGGGATTGGACCTTTGCGAAGCAACGCCCGGGGGGGTGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCa                                                                             <  2:674542/151‑1 (MQ=11)                                                                                    ctcCGGAGTAGGAAAAACCCGCGGGGGGGGGTTTTAAACTTTGCAAAGCAAGGGCCGGGGGGGTGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGgc                                                                        <  2:539184/146‑1 (MQ=11)                                                                                           gTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAAt                                                            >  2:459977/1‑151 (MQ=255)                                                                                             aGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGc                                                          >  2:769246/1‑151 (MQ=255)                                                                                              gaaaaaaCCCGCGGGGAGGGGATTTGAACGTTGCGAAGCAACGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGaaaaa                                                               <  1:25866/141‑1 (MQ=14)                                                                                               gACAAACCCGCGGGGGGGGGTTTTGAACCTTGAGAAGACGCGCCCCGGAGTGTGGGGGGCAGCACCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAAt                                                            <  1:647420/147‑1 (MQ=14)                                                                                                aCAAACCCGCGGGGGGCGGATTTGAACTTTGGAAACCAACGCCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAAt                                                            <  1:911708/146‑1 (MQ=14)                                                                                                  aactcggggggggGCGGATTTAACTGTTGAGAAGCAACGGCCCGGGGGGGGGGGGGAAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGc                                                          <  2:522819/137‑1 (MQ=14)                                                                                                  aaccccgcggGGAGCGGATTGAAACGTTGCGAAGCAACGGCCGGGGGGGGGGCGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCgg                                                       <  2:90855/145‑1 (MQ=17)                                                                                                           ggggGCGGATTTGACCGTTGCGAAGCAGCGGCCGGGAGGGGGGGGGGCAGGGCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCt                                             <  2:858429/150‑1 (MQ=17)                                                                                                              aGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGgcg                                         >  1:410251/1‑151 (MQ=255)                                                                                                               ggggATTTGAACGTTGCGAAGCAACGGCGGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGgcgc                                        <  2:735324/149‑1 (MQ=18)                                                                                                               ggggATTTGAACGTTGCGAAGAAAGGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGgcgc                                        <  1:736750/149‑1 (MQ=18)                                                                                                                cGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGcgcg                                       >  2:533932/1‑151 (MQ=255)                                                                                                                 ggATTTGATCTTTGCAAAGCACCGGCCGGGGGGGGGGGGGGAGGGCCCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGt                                      <  2:92831/151‑1 (MQ=18)                                                                                                                 ggATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGt                                      >  2:462624/1‑151 (MQ=255)                                                                                                                        aaCGTTGCGAAGCAACGGCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTAt                                 <  1:681091/149‑1 (MQ=255)                                                                                                                        aaCGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAACTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATcc                               >  1:8173/1‑151 (MQ=255)                                                                                                                         aCGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATcc                               >  1:904799/1‑150 (MQ=255)                                                                                                                            ttGCAAAGCAACGGCCCGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCa                              <  1:587990/148‑1 (MQ=255)                                                                                                                             ggCGAAGCAGCGGCCGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGcc                           <  2:212804/149‑1 (MQ=21)                                                                                                                                 aaGCAGCGGCCGGGGGGGGGGGGGGCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTAct                       <  1:755852/150‑1 (MQ=21)                                                                                                                                       cGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCtt                >  1:169178/1‑151 (MQ=255)                                                                                                                                        ggCCGGGGGGGTGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCt                 <  1:446381/149‑1 (MQ=255)                                                                                                                                        ggCCGGGGGGGGGGGGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTa               <  2:639818/151‑1 (MQ=255)                                                                                                                                        ggCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCtt                >  1:661106/1‑150 (MQ=255)                                                                                                                                          cgggggggggggggggCAGGCCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCtt                <  1:173426/142‑1 (MQ=255)                                                                                                                                          ccgggggggTGGGGGCCCGCACCCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTa               <  2:161765/143‑1 (MQ=21)                                                                                                                                          ccgggggggTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGTATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTAt              <  1:514009/144‑1 (MQ=255)                                                                                                                                             gggggggggggggCAGGGCGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTAt              <  1:204575/144‑1 (MQ=255)                                                                                                                                                     gCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCttt  >  2:504193/1‑151 (MQ=255)                                                                                                                                                      |                                                                                                                                                      GAACTGCCAGGCATCAAATAAAACGAAAGGCTCAGTCGGAAGACTGGGCCTTTCGTTTTATCTGTTGTTTGTCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAACTGCCAGGCATCAAATTAAGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCATTGGCGCAGAAAAAAATGCCGGATGCGACGCTGGCGCGTCTTATCCAGCCTACTCTTGCTTATCCGTTCTGCTTT  >  NC_000913/4040623‑4040921

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑