Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	47.5%	30.7 / 31.1	40	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (7/14);  new base T (19/0);  total (26/14)
Fisher's exact test for biased strand distribution p-value = 5.51e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCAGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413586‑1413883                                                                                                                                                      |                                                                                                                                                     aTCAGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTta                                                                                                                                                      <  1:136314/150‑1 (MQ=255)         tACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATGaa                                                                                                                                              >  2:904438/1‑150 (MQ=255)         tACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGaa                                                                                                                                              <  2:307716/150‑1 (MQ=255)             ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATCCATGAACAcc                                                                                                                                          <  1:729117/150‑1 (MQ=255)              tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATTAAAAcccc                                                                                                                                        >  2:343914/1‑149 (MQ=255)                       tGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAAAACCTCCcttatttt                                                                                                                               >  1:64721/1‑149 (MQ=255)                        ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattattat                                                                                                                               <  1:843239/150‑1 (MQ=255)                        ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattatt                                                                                                                                 <  1:298961/148‑1 (MQ=255)                         gAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTATTAATTTACACCCCCCTtttttttt                                                                                                                             >  1:178370/1‑151 (MQ=255)                                   cttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGGAACTTTTTATTTAAACACCTCCATtttttttttccgttggtt                                                                                                                   >  2:405935/1‑141 (MQ=255)                                            tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAACAACTCCCCTATTATTTTCAGGGGTTCGttttttt                                                                                                           >  2:758715/1‑149 (MQ=255)                                            tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGGTATTTTTTTAATGAAAACCTCCCTTTTTTTTTTCACTGGGTTGtttttt                                                                                                            >  2:1000589/1‑149 (MQ=255)                                              ccTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATAAAAACCTCCATTTTTATTTTCAGTGGGTTGttttt                                                                                                             >  2:205155/1‑144 (MQ=255)                                                        ttttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATTAAAACCCCCATTATTTTTTTTATTGGTTTGttttttttctcttt                                                                                                    >  1:620538/1‑137 (MQ=255)                                                           tttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATTGAAACCTCCATTATTATTTTCAGTGGGTTGTTTTTTTCATCTTTTGTGTGctt                                                                                           >  2:910009/1‑151 (MQ=255)                                                            ttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGctt                                                                                           <  2:411939/150‑1 (MQ=255)                                                                cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAGCACCCCCCTTTTTTTTTTCAGTGGTTTGTTTTTTTTTTCTTTTTTGTGCTtttttt                                                                                      >  1:244828/1‑151 (MQ=255)                                                                 aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCttttt                                                                                     <  1:673635/151‑1 (MQ=255)                                                                 aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCttttt                                                                                     <  2:968161/151‑1 (MQ=255)                                                                     tGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTAAATAAACAACCCCATTTTTTTTTTTATTGGGTAGTTTTTTTTATCCTTTGAGGGCTTCttttt                                                                                     >  1:1000101/1‑147 (MQ=255)                                                                      gATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTTCATTAAAAACTCCCTTTTTATTTTCCGTGGGTTGTTTTTTTCCTCTTTTTAGGGCTTCtttttttttt                                                                                >  2:873635/1‑146 (MQ=255)                                                                         ttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATTAAAACCCCCATTTTTTTTTTCAGTGGGTTGTTTTTTTCATTTTTTTAGTGCTTCtttttttttttc                                                                              >  1:964735/1‑143 (MQ=255)                                                                          tCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAAAACCTCCCTTTTTATTTTCAGTGGGTTGTTTTTTTCATCTTTTGAGTGCttttttttttctttc                                                                              >  2:10293/1‑142 (MQ=255)                                                                          tCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTcca                                                                             <  2:277401/150‑1 (MQ=255)                                                                                gTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATAAACACCCCCCTTTTTATTTCCCTTGGTTCGGTTTTTTCATTTTTTTAGTGCTTCTTTTTTACTTCCACCATaa                                                                       >  1:310121/1‑150 (MQ=255)                                                                                    aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTAATTAAAACCCCCCCTTTTTTTTTCCGTGGGTTGTTTTTTTCCTCTTTTTAGGGCTTTTTTTTTTCTTCCCCCCTaaaccg                                                                   >  1:719128/1‑146 (MQ=255)                                                                                    aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTAAATTAAAAACCCCCCTTTTTTTTTCAGTGGGTCGTTTTTTTCATCTTTTTCGTGGTTCTTTTTTTCTTCCCCCATaa                                                                       >  2:1033993/1‑146 (MQ=255)                                                                                    aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGt                                                                  <  2:192511/151‑1 (MQ=255)                                                                                          tGAATGTCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAAAACCCCCCTTTTTATTTTCAGTGGGTTGTTTTTTTCATCTTTTTAGGGCTTTTTTTTTTCTTTCACCCTAAACCGGTCgggg                                                            >  2:912772/1‑150 (MQ=255)                                                                                            aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATAAATGAACACCCCCCTTTTTTTTTTTCGTGGGTGGTTTTTTTTTTTTTTTCAGTTCTTCTTTTTTTCTTTCCCCCTAAACCGTTCTGGGtt                                                          >  1:562425/1‑151 (MQ=255)                                                                                                    gTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATcc                                                   <  2:44013/150‑1 (MQ=255)                                                                                                       cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATGAACACCCCCATTATTTTTTTCAGTGGGTCGTTTTTTTCATCTTTTTAGTGCTTCTTTTTTTCTTTCACCCTAACCCGGTCGGGGTTTGCATcc                                                   >  2:994124/1‑147 (MQ=255)                                                                                                        aGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTac                                              <  2:950333/151‑1 (MQ=255)                                                                                                               agGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGc                                       <  2:412426/151‑1 (MQ=255)                                                                                                                                tttCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaa                       <  1:828326/150‑1 (MQ=255)                                                                                                                                            cGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCg          >  1:1009208/1‑151 (MQ=255)                                                                                                                                             ggTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGt         >  1:587130/1‑151 (MQ=255)                                                                                                                                              gTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTTACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGtt        >  1:637241/1‑151 (MQ=255)                                                                                                                                                aaTTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTa       <  2:632166/150‑1 (MQ=255)                                                                                                                                                aaTTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTAc      >  2:126109/1‑151 (MQ=255)                                                                                                                                                    ttATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt  >  1:306814/1‑151 (MQ=255)                                                                                                                                                     tataCATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt  <  2:587525/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     ATCAGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413586‑1413883

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑