Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	689,514	0	A	C	43.2%	56.1 / 11.5	37	G456G (GGT→GGG)	lnt	apolipoprotein N‑acyltransferase
Reads supporting (aligned to +/- strand):  ref base A (17/4);  new base C (0/16);  total (17/20)
Fisher's exact test for biased strand distribution p-value = 5.89e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCAACACAGCAGCAAAACCAAACAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATCGTTGGAG  >  NC_000913/689367‑689652                                                                                                                                                     |                                                                                                                                           catcaACACAGCAGCAAAACCAAACAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCAcc                                                                                                                                          <  1:576988/150‑1 (MQ=255)         cagcagAAAAACCAAACAAGGCCGGCAGCGCCCACAGCGGCCAGGTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCggg                                                                                                                                   <  2:850376/149‑1 (MQ=255)                 aaaCCAAACAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCCCCCTGCGGGCCAATCAccg                                                                                                                         <  2:954987/151‑1 (MQ=255)                 aaaCCAAACAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACATGCGTATGGTGTAGATCTCGGTGGTCGCCGTATCATTA‑AAATAAAAACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATATCACCCTGAGGGACAATCAcc                                                                                                                          >  2:586692/1‑150 (MQ=255)                      aaaCAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑AGATCTGGTGGGCCGCCGCACCATTAAGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGt                                                                                                                     >  2:757075/1‑150 (MQ=255)                            tGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCCGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCg                                                                                                              >  2:214854/1‑151 (MQ=255)                               cGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCgttg                                                                                                           >  1:710904/1‑151 (MQ=255)                                       cccACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGTTAAACCCCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCCCCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGtgc                                                                                                    <  1:623878/150‑1 (MQ=255)                                               ggCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAAc                                                                                            >  1:667576/1‑150 (MQ=255)                                                   aGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCGCGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTgg                                                                                       >  1:158929/1‑151 (MQ=255)                                                     ttGCCGGTACGTGCGTATGGTGT‑GAGTCGGGTGGTCGGCGCCACGTTAGTGGTTAACCCCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTggg                                                                                      <  1:296778/150‑1 (MQ=255)                                                          gttACGTGCGTATGGTGG‑GAGTCCGGTGGTCGGCGTCACTTTAGTGGTAAACACCTCGCGGGTGAACTGGGGGATCATCGCCTGAATCTCCCCCTGCGGCCAAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGgcg                                                                                    <  1:339659/145‑1 (MQ=255)                                                           gTACGTGCGTATGGTGT‑GAGTCGGGTGGTCGGCGTCACTTTGGTGGTTAACCCCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCCCCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCa                                                                               <  1:292178/151‑1 (MQ=255)                                                                    tgtggtgg‑GAGTCGGGTGGGCGGCGTCACGTTAGTGGTTAACCCCGCGCGGGTGATCTGGGGGATCATCCCCTAAACCTCCCCCTGCGGCCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGc                                                                             <  2:573668/142‑1 (MQ=255)                                                                    gtgtggggggggTCCGGTGGTCGGCGTCACGTTGGTGGTTACCACCTCGCGGGTGACCGGGGGGATCATCGCCTTAATCTCCCCCTGCGGGCCAAGCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAgc                                                                       <  2:899730/140‑1 (MQ=255)                                                                          gt‑gAGTCGGGTGGTCGGCGTCACTTTAGGGGTAAACCCCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCCCCCCCGGCGGCCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGcgcacg                                                                  <  2:187774/149‑1 (MQ=255)                                                                           t‑gAGTCCGGTGGTCGGCGTCACGTTAGTGTTTAACCCCTCGCGGGTGATCTGCGGGATCATGGCCTGAATCTCCCCCTGCGGGCAAATCCCCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGcgcacgc                                                                 <  1:236168/149‑1 (MQ=255)                                                                           gggAGTCCGGTGGTCGGGGTCACTTTAGTGGTTAACACCTCGGGGGTGAACTGGGGGATCAGCGCCTGAATCCCCCCCGGGGGGCAAACCCCCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGcgcacg                                                                  <  2:533097/147‑1 (MQ=255)                                                                              aGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTc                                                             >  2:419051/1‑151 (MQ=255)                                                                                 cggggggtGGGCGTCCCTTTTGTGTTAAACCCTTCGCGGGTAAATTGGGGGATCATCGCCTGAATCTCCCCCGGGGGGCCATTCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTcgc                                                           <  1:338587/145‑1 (MQ=255)                                                                                   ggtggtGGGGGTCCCGTTAGTGGTTAACCCCGCGGGGGTAAACTGCGGGATCATCGCCTGAATCTCCCCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTc                                                             <  2:751631/146‑1 (MQ=255)                                                                                      ggtCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATc                                                     >  1:721122/1‑151 (MQ=255)                                                                                         cGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTgg                                                  >  2:643137/1‑151 (MQ=255)                                                                                          ggCGCCACGTTGGTGTTTAACACCTCGGGGGTGAACTGCGGGATCATCGCCGGAATCTCCCCCGGCGGGCAAATCCCCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTg                                                   <  2:768928/149‑1 (MQ=255)                                                                                               cACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGTCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAgtg                                             >  2:683961/1‑150 (MQ=255)                                                                                               cACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAgtgt                                            >  1:419820/1‑151 (MQ=255)                                                                                                aCGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGtt                                           >  1:353663/1‑151 (MQ=255)                                                                                                  gTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGc                                         >  2:689771/1‑151 (MQ=255)                                                                                                   ttAGTGATTAACTGCTCGCGGGCAAATTGGGGAACCATCGCCTGACTCTCCCCCTGCGGGACAATCCCCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAgtg                                             <  2:29654/146‑1 (MQ=255)                                                                                                     aGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCAt                                      >  1:635919/1‑151 (MQ=255)                                                                                                                           aaCTGGGGGACCACCCCCTGACTCCCACCCGGCGGGCCACCCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCaa                   <  2:207358/148‑1 (MQ=255)                                                                                                                           aaCTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAAcc                >  1:220761/1‑151 (MQ=255)                                                                                                                               gCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGc            >  2:646665/1‑151 (MQ=255)                                                                                                                                      cctcgctgacacctcCCCCTGCGGGCCAGACACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATCGTTg     <  2:793360/139‑1 (MQ=255)                                                                                                                                      catcGCTTGAATCCCCCCCTGCGGCCAAGTCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATc         <  2:902269/147‑1 (MQ=255)                                                                                                                                      catcGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATCGTTg     >  1:664808/1‑151 (MQ=255)                                                                                                                                           cttGAATCTCCCCCGGCGGGCCAACCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATCGTTGgag  <  2:104458/147‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                           CATCAACACAGCAGCAAAACCAAACAATGCCGTCAGCACCCACAGCGGCCAGTTGCCGGTACGTGCGTATGGTGT‑GAGTCCGGTGGTCGGCGTCACGTTAGTGGTTAACACCTCGCGGGTGAACTGCGGGATCATCGCCTGAATCTCACCCTGCGGGCCAATCACCGCCGTAATGCCGTTGTTGGTGCTGCGCAACAGTGGGCGCGCCAGCTCCAGCGCACGCATTCGCGCCATCTGGAAGTGTTGCCATGGACCAATAGATTTACCAAACCACGCATCGTTGGAG  >  NC_000913/689367‑689652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑