Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,378,802	0	A	C	56.7%	28.5 / 46.9	30	V48G (GTA→GGA)	ampC	penicillin‑binding protein; beta‑lactamase, intrinsically weak
Reads supporting (aligned to +/- strand):  ref base A (13/0);  new base C (0/17);  total (13/17)
Fisher's exact test for biased strand distribution p-value = 8.35e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.99e-07

CCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTT  >  NC_000913/4378653‑4378938                                                                                                                                                        |                                                                                                                                         ccccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTac                                                                                                                                         >  2:224915/1‑151 (MQ=255) ccccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTac                                                                                                                                         <  1:637057/151‑1 (MQ=255)  cccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTacc                                                                                                                                        >  2:405366/1‑151 (MQ=255)   ccTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccg                                                                                                                                       >  1:821259/1‑151 (MQ=255)      cGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccgcca                                                                                                                                    <  1:222186/151‑1 (MQ=255)      cGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccgcc                                                                                                                                     <  2:842219/150‑1 (MQ=255)      cGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccgcc                                                                                                                                     >  1:363999/1‑150 (MQ=255)       gAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccgccac                                                                                                                                   >  2:509962/1‑151 (MQ=255)          cAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTaccgccaccgc                                                                                                                                >  2:474616/1‑151 (MQ=255)                        ccaAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCt                                                                                                                  >  1:486008/1‑151 (MQ=255)                        caaaGCCCGCCAGAAAATTTTTTGCTGCCCAAACCAAACTA‑AAACACCGTTTGTTGTGTGCGGGGTTGTTTTTGGGCGATGCCCGCATACCCCCAGGAAAAGAAATAAGTTTTCCCT‑TAATAAATTCCCGCCACCGCCATACCCGGGATCt                                                                                                                  <  1:537315/149‑1 (MQ=255)                          aaccccGCAAGTAATTGTTTTGCTGACAAACCCTAACAA‑AAACAACTTTTGCTGTGTGGCGGGCTGTTTTTTGGCGATGTCCGCATACCCCCAGAAAAATAAAAAAGTTTTCCCC‑TAAAAAATTCCCGCCACCGCCATACCCGGGATCt                                                                                                                  <  1:611170/144‑1 (MQ=255)                                gCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGCTTGCTGCGTGACGGGCTGCTTTTCGGCGATGCCCGCATAGCCCCAGGTAAAGTAATACGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTttgttg                                                                                                           >  2:775597/1‑150 (MQ=255)                                      aatttttttGCTGACCGACCCTAACTA‑AAACAACGTTTGCTGTGTGAGGGGTTGTTTTTTGGCGATGTCCGCAAAGCCCCAGGAAAAGTAATAGGTTTTCCCT‑TGAAAATTTCCCGCCACCGCCATACCCGGGATCTTTTGTTGc                                                                                                          <  1:216072/140‑1 (MQ=255)                                       atttttttGCTGA‑CGCACCTAACCCAAAACAAGGTTTGCTGTTTGCGGGGTTGTTTTTGGGGGTTGCCCGCAAAGCCCAAGTAAAAAAAATAAGTTTTCCCA‑TTATAATTACCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATaa                                                                                                   <  1:790293/147‑1 (MQ=255)                                       atttttttGCGGACCAAACCTAACTA‑AAACACCGTTGGTTGTGTGAGGGGCTTTTTTTTGGCGATGCCCGCATACCCCCAGGAAAATTAAAAAGTTTTCCCC‑TAAAAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATaa                                                                                                   <  2:921620/147‑1 (MQ=255)                                                         ccTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGAt                                                                                 >  1:624361/1‑151 (MQ=255)                                                            aaCTA‑AAACAACGTTTGCTGTGTGAGGGGTTGTTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGAAATAAGTTTTCCCC‑TAATAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATg                                                                                <  1:790561/149‑1 (MQ=255)                                                                   aacaccTTTTGCTGTGTGGGGGGTTTTTTTTGGGCGTTGCCCGCATACCCCCAGGAAAAGAAAAAGGGTTTCCCC‑AAAAAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAatat                                                                        <  1:39001/151‑1 (MQ=255)                                                                          tttGTTGGGTGGCGGGCTGTTTTTGGGCGTTCCCCGCAAACCCCAAGTAAAAGAAATAATTTTTCCCC‑TGAAAATTTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGtt                                                                    <  2:369193/148‑1 (MQ=255)                                                                            tGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGAttt                                                               >  1:760403/1‑151 (MQ=255)                                                                              cTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGTCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttgt                                                             >  2:488817/1‑151 (MQ=255)                                                                                 tgtgAGGGCCTTTTTTTGGGCGTTGTCCGCATACCCCCAGGAAAAAAAAAAGTGTTTCCCC‑TAAAAATTCCCCCCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATttg                                                              <  1:415348/147‑1 (MQ=255)                                                                                   tggcGGGGTGTTTTTGGGAGATGCCCGCATAGCCCCAGAAAAAAAAAAAAGTTTTCCGC‑TAATAATTTCCCCCCGCCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAg                                                         <  1:877972/147‑1 (MQ=255)                                                                                        ggtttttttttGGCGTTGTCCGCTCACCCCCAGTTAAATTAATAAGGTTTCCCT‑TAATAATTTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGgcag                                                   <  1:489549/145‑1 (MQ=255)                                                                                          tttttttttGGCGATTTCCGCTTGCCCCCGGGAAAAGTAAAAAGGTTTCCCT‑TAATAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGgcagc                                                  <  2:897707/146‑1 (MQ=255)                                                                                            gctTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCaa                                                >  1:465337/1‑150 (MQ=255)                                                                                                   ggtggttcccGCATTCCCCCA‑GTAAAGGAAAAAAGTTTCCCCGTTATAATTCCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAAtgtg                                           <  2:524474/140‑1 (MQ=255)                                                                                                                 aGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaat                          >  2:459470/1‑151 (MQ=255)                                                                                                                     caagaaaaaGTAAAAGGTTTTCCCC‑TGATAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGtaattaat                      <  1:656668/145‑1 (MQ=255)                                                                                                                       agatAAAGTAATAAGTTTTCCCT‑TAATAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATtaata                     <  1:476910/147‑1 (MQ=255)                                                                                                                        ggTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGTGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATtaata                     >  1:267587/1‑149 (MQ=255)                                                                                                                          tAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgc                 >  1:483340/1‑151 (MQ=255)                                                                                                                           aaaGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAgg                  >  2:919412/1‑149 (MQ=255)                                                                                                                             aGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGgcg                >  2:1961/1‑149 (MQ=255)                                                                                                                                 ataaGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCagag           >  2:816310/1‑150 (MQ=255)                                                                                                                                     agttctcccttGATAATTACCCGCAACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCaga            <  2:275073/136‑1 (MQ=255)                                                                                                                                        ttcccc‑TAAAAAATTCCCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtt    <  1:87772/147‑1 (MQ=255)                                                                                                                                         tACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGtttt  >  1:84270/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                         CCCCTCGAGCAATAGCGTCGCCACCAAGCACGCCAGTAAATGTTTTGCTGACCGAACCTAACTC‑AAACAACGTTTGCTGTGTGACGGGCTGCTTTTTGGCGATGTCCGCATAGCCCCAGGTAAAGTAATAAGGTTTACCC‑TGATAAATTACCGCCACCGCCATACCCGGGATCTTTTGTTGCTCTATAAGCGGGGTAATTGTGCGATGCACAATATCGTTGATTTGTTGAGGGGCAGCAAATGTGGAGCAAGAGGCGGTAATTAATAAGGCGCAGAGCGTCGTTTT  >  NC_000913/4378653‑4378938

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: ‑