Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,544,546	0	T	G	30.4%	51.2 / 37.1	46	intergenic (+63/+51)	mdfA/ampG	multidrug MFS transporter/muropeptide permease AmpG
Reads supporting (aligned to +/- strand):  ref base T (12/20);  new base G (7/7);  total (19/27)
Fisher's exact test for biased strand distribution p-value = 5.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.24e-01
Rejected as consensus: Frequency below/above cutoff threshold.

GCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCACCC  >  NC_002947/1544400‑1544694                                                                                                                                                   |                                                                                                                                                     gcggGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGt                                                                                                                                                   <  2:210225/150‑1 (MQ=255)       gTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGc                                                                                                                                             <  2:502637/150‑1 (MQ=37)         ggCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCgg                                                                                                                                           <  1:891572/150‑1 (MQ=255)          gCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCggg                                                                                                                                          <  2:385786/150‑1 (MQ=25)               ggCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTAc                                                                                                                                     <  1:60104/150‑1 (MQ=255)                gCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTAcc                                                                                                                                    >  2:667903/1‑150 (MQ=255)                   ttGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCcgc                                                                                                                                 <  1:667903/150‑1 (MQ=255)                      gcgcTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAACCCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGaa                                                                                                                              <  2:990354/150‑1 (MQ=255)                      gcgcTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGaa                                                                                                                              <  1:335182/150‑1 (MQ=255)                         cTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAagag                                                                                                                           <  1:1063559/150‑1 (MQ=21)                           gtgGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAGGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGc                                                                                                                         <  2:690618/150‑1 (MQ=255)                            tgGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGcc                                                                                                                        >  1:492969/1‑150 (MQ=255)                              gCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCgg                                                                                                                                           >  1:426619/1‑129 (MQ=255)                              gCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCgg                                                                                                                                           <  2:426619/129‑1 (MQ=255)                                   tgtgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAg                                                                                                                 <  2:1038350/150‑1 (MQ=255)                                    gtgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAgg                                                                                                                <  1:403750/150‑1 (MQ=255)                                    gtgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCgg                                                                                                                                           >  2:291232/1‑123 (MQ=21)                                    gtgGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCgg                                                                                                                                           <  1:291232/123‑1 (MQ=21)                                                    gggCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAg                                                                                                <  2:492969/150‑1 (MQ=255)                                                     ggcggcTGGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAgg                                                                                               <  1:196865/150‑1 (MQ=255)                                                              gggAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAg                                                                                      >  1:928284/1‑150 (MQ=255)                                                                              tCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGgtcgtc                                                                      >  1:707179/1‑150 (MQ=255)                                                                                      cGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCg                                                              <  2:707179/150‑1 (MQ=255)                                                                                                    ctggccTCTTCGCGGGTAAACCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCcccgcccg                                                >  1:1182240/3‑150 (MQ=18)                                                                                                    ccggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCcccgcccg                                                <  2:567602/150‑1 (MQ=255)                                                                                                     cggccTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCAAGGCGGTGAACTGGAGTTTTTCTGGACCGGCTAGCCACCGAGTGGTCGACCGCCACCCGCGTCCcccgccgcg                                               >  1:148377/1‑147 (MQ=12)                                                                                                            ttCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGc                                                                                                                                             >  2:1193162/1‑49 (MQ=255)                                                                                                            ttCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGc                                                                                                                                             <  1:1193162/49‑1 (MQ=255)                                                                                                                 gggTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGcc                                   >  1:512967/1‑150 (MQ=255)                                                                                                                  ggTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCa                                  >  1:1109870/1‑150 (MQ=255)                                                                                                                  ggTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCa                                  <  2:928284/150‑1 (MQ=255)                                                                                                                    tAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACt                                <  2:1109870/150‑1 (MQ=255)                                                                                                                       aCCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCgg                                               <  1:920233/132‑1 (MQ=21)                                                                                                                       aCCCGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCgg                                               >  2:920233/1‑132 (MQ=21)                                                                                                                         ccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTcc                                          >  2:18580/1‑135 (MQ=255)                                                                                                                         ccGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTcc                                          <  1:18580/135‑1 (MQ=255)                                                                                                                         ccGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCCGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGCTGCCCCTGCAgg                           >  2:606863/1‑150 (MQ=18)                                                                                                                         ccGCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAgg                           >  2:628741/1‑150 (MQ=25)                                                                                                                           gCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGc                         >  1:437729/1‑150 (MQ=255)                                                                                                                           gCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGAt                                      >  2:1027162/1‑137 (MQ=25)                                                                                                                           gCTCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGAt                                      <  1:1027162/137‑1 (MQ=25)                                                                                                                             tCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCga                       >  1:49466/1‑150 (MQ=255)                                                                                                                             tCCTACAAAGCGGCGCGGCCCTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCga                       >  1:492062/1‑150 (MQ=37)                                                                                                                                   aaagcggcgcggcccTGTGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCCCCGGCAATACCAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCgatcagga                 <  2:847382/143‑1 (MQ=25)                                                                                                                                        gctgtgccgcTTTGTGGGAGCTCGTGTAGCCGCGAAGAGGCCAGCACAGACAATACAAAGCGTCAGGGCCGCGCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGc            <  2:512967/145‑1 (MQ=255)                                                                                                                                           gcgccgcTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTa         <  2:49466/150‑1 (MQ=255)                                                                                                                                                  tttGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCAccc  >  1:969126/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                     GCGGGGGTGGCGGGGGCGTTGGCGCTGTGGCCGCTGTGGTTTGTGGTGGGTGGGCGGCCTGGGGAAGGGGCTGTAGCTCGATAATCGGTATTGCCGGGGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACACAGGGCCGCGCCGCTTTGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGCACAGGCAATACAAAGCTTCAGGGCCGCTCAGCCACCGAGTGGTCGTCCGCCACCGGCGTCCCCCGCCCGGCTTCCTGATGCCACTGCAGGGCGATCAGGATCAGCGTAGGCACCC  >  NC_002947/1544400‑1544694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑