Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	45.2%	50.7 / 25.9	42	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (3/20);  new base T (19/0);  total (22/20)
Fisher's exact test for biased strand distribution p-value = 3.49e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413595‑1413881                                                                                                                                             |                                                                                                                                                    aCTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAaca                                                                                                                                           <  2:518195/151‑1 (MQ=255)        gCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTc                                                                                                                                       <  1:905148/148‑1 (MQ=255)           ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCatt                                                                                                                                   <  2:21919/149‑1 (MQ=255)           ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTACAATAacaacccc                                                                                                                                      >  2:747949/1‑141 (MQ=255)             ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATTAAAACCTCCcttttt                                                                                                                                >  2:314167/1‑150 (MQ=255)               ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattatt                                                                                                                                <  2:673481/148‑1 (MQ=255)                  aaCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAAATAACACCCCCCTtttttttt                                                                                                                            >  1:523846/1‑149 (MQ=255)                  aaCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTcc                                                                                                                          <  2:62401/151‑1 (MQ=255)                   aCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCa                                                                                                                         <  1:251124/151‑1 (MQ=255)                             cttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATTAACACCCCCCTtttttttttccctgggttgtt                                                                                                               >  1:663495/1‑138 (MQ=255)                               tttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAAATTACAACTCCATTAttttttttagcgggttgttt                                                                                                              >  1:361352/1‑136 (MQ=255)                                ttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATTAACACCCCCCTTTTTATTTTCAGTGGttgtttttt                                                                                                            >  1:267575/1‑144 (MQ=255)                                 tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACAACCCCCTTATTTTTTTCCGTGGTTCGTTTAtt                                                                                                           >  1:291991/1‑151 (MQ=255)                                 tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTAt                                                                                                            <  2:110956/150‑1 (MQ=255)                                       tGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTTAATTAAAACCTCCCTTATTTTTTTCCGTGGTTCGtttttttc                                                                                                         >  1:269067/1‑145 (MQ=255)                                        gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTATATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACACCTCCCTTTTTATTTCCAATGGGTTGTTTATTTcttctt                                                                                                    >  2:242140/1‑151 (MQ=255)                                        gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCtt                                                                                                    <  1:225710/151‑1 (MQ=255)                                          gagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAAAACCTCCATTTTTATTTTCAGTGGTTCGTTTTTTTCATCttt                                                                                                   >  2:389183/1‑150 (MQ=255)                                           agCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAAAACCTCCCTTTTTTTTTTCCGTGGGTTGTTTTTTTCTTCttt                                                                                                   >  1:684063/1‑149 (MQ=255)                                             cATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAg                                                                                               <  1:330567/151‑1 (MQ=255)                                              aTTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAAAACCTCCCTTTTTATTTTCAGTGGGTTGTTTTTTTCCTCTTTCgtg                                                                                               >  2:368269/1‑148 (MQ=255)                                              aTTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAACAACTCCCTTATTTTTTTCCGTGGGTCGTTTTTTTCCTCtttttag                                                                                               >  2:39935/1‑146 (MQ=255)                                                       cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑tttt                                                                                    <  2:530737/151‑1 (MQ=255)                                                          tCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATAAATGTACACCCCCCTTATTATTTTTTGTGGGTCGTTTTTTTCATCTTTTTAGGGGTTC‑ttttt                                                                                   >  1:723733/1‑149 (MQ=255)                                                              aTTTCGTTAGTTTAGATGTTGAATATCTTGTCCAGTTAGTAGGAGTGCCGCCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACtt                                                                              <  1:374886/150‑1 (MQ=255)                                                                    ttAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGAAATTTTTTAAATAAAAAACCCCATTTTTATTTTCACTGGGTTGTTTTTTTCTTCTTTTGAGTGTttt‑tttttttct                                                                               >  1:787595/1‑139 (MQ=255)                                                                         ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAAcc                                                                   <  1:986242/150‑1 (MQ=255)                                                                         ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAAcc                                                                   <  1:384636/150‑1 (MQ=255)                                                                          tAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAACACCTCCCCTTTTATTTTCCGTGGGTCGTTTTTTTCATCTTTCGAGTGCTTT‑TTTTTTACTTCCCCCATAAACgg                                                                 >  2:695655/1‑151 (MQ=255)                                                                                   aaTATCTTGTCCAGTTAGTAGGAGTGTCACCATCCTTTTCAATAGTAGCAGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCgg                                                            <  1:141426/147‑1 (MQ=255)                                                                                    atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACACCCCCCTTTTTTTTTTCAGTGGGTCGTTTTTTTCCTCTTTTTAGTGCTTC‑TTTTTTTCTTTCCCCCTAAACGGTTTggg                                                           >  1:274874/1‑147 (MQ=255)                                                                                         ttGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGCAAATTTTTATATGAAAACCTCCCCTTTTATTTTCCGTGGTTTGTTTTTTTCATCTTTTCGGTGCTTT‑TTTTTTTCTTCCCCCCTAAACCGTTTggggt                                                         >  1:530814/1‑142 (MQ=255)                                                                                             ccAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGtt                                              <  1:110905/151‑1 (MQ=255)                                                                                             ccAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGt                                               <  1:617043/150‑1 (MQ=255)                                                                                              cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTTCACTTAGACCTCCATTTATCTTTCCTGTCGGTCCTTTTATCCATCTTTTCTGCGTTTCTTTTTTAACTTCC‑CCCTAAACGCTTCTGGATTTGcc                                                    >  2:975288/1‑143 (MQ=255)                                                                                                                 cttccttTTCAATAGTGGCGGTAATTTTTTAAAAGAACACCTCCCTTATTATTTTCAGTGGTTTGTTTTTTTCCTCTTTTGAGTGGTTT‑TTTTTTTCTTTCCCCCTAACCCGTTTGGGGTTTGCATCCCTTACACCTCCCTCGGGaa                              >  2:533419/1‑147 (MQ=255)                                                                                                                          cAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATg                  <  1:910939/150‑1 (MQ=255)                                                                                                                          cAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATg                  <  2:539309/150‑1 (MQ=255)                                                                                                                                tGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCttt             >  2:725713/1‑149 (MQ=255)                                                                                                                                    ggTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGt       <  1:730428/151‑1 (MQ=255)                                                                                                                                        aTTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACt   <  1:199124/151‑1 (MQ=255)                                                                                                                                         ttttATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg  >  2:54537/1‑151 (MQ=255)                                                                                                                                             |                                                                                                                                                    ACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413595‑1413881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑