Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	54.2%	10.6 / 36.3	24	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (0/11);  new base T (13/0);  total (13/11)
Fisher's exact test for biased strand distribution p-value = 4.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-06

AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413589‑1413883                                                                                                                                                   |                                                                                                                                                     aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACa                                                                                                                                                  <  1:138124/151‑1 (MQ=255)           tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGCATAcccc                                                                                                                                        >  1:285309/1‑149 (MQ=255)                   ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAAAGAAAACCTCCcttatt                                                                                                                                 >  1:461566/1‑150 (MQ=255)                    tGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATAATAACAACTCCcttttt                                                                                                                                 >  2:519878/1‑149 (MQ=255)                         aCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTGCCTTTTCAATAGTGGCGGTAATTTTATACATGAACTCCTCCATTATTATTTcc                                                                                                                           <  2:638821/150‑1 (MQ=255)                          cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATTAAAAACTCCCTtttttttttccg                                                                                                                         >  1:533514/1‑147 (MQ=255)                                 ttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGCAATTTTTTACATTAACACCCCCCTTATTTTTTTCATTgg                                                                                                                      >  1:516862/1‑147 (MQ=255)                                           ccTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAAATAACACCTCCCTTTTTTTTTTCAGTGGtttggttttt                                                                                                            >  2:516101/1‑139 (MQ=255)                                                gagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTc                                                                                                   <  1:688066/151‑1 (MQ=255)                                                      tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTg                                                                                              <  1:239006/150‑1 (MQ=255)                                                            gCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATTAAAACCCCCCTTATTATTTTCAGTGGGTCGTTTTTTTCATCTTTTTTGTGCtttttt                                                                                       >  1:523616/1‑151 (MQ=255)                                                              aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTCATTTTTTATATTGATACCCCCCTTTTTATTTTTCGCGGGTGGTTTTTTTCCTCTTTTTTGTGCTTCttttt                                                                                     >  2:248736/1‑151 (MQ=255)                                                              aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATAAGAACAACCCCCTTTTTTTTTTCAGTGGTTCGTTTTTTTCCTCTTTTTAGTGCtttttttt                                                                                     >  1:838423/1‑151 (MQ=255)                                                                            aGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATaa                                                                       <  1:516129/151‑1 (MQ=255)                                                                                      ttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCgg                                                              <  1:722400/150‑1 (MQ=255)                                                                                       tGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTAACATGAATACCTCCCTTATTTTTTTCAGTGGGTGGTTTGTTTCATCTTTTCAGTGATTCTTTTTTACTTTCTCCACAAACGGTTCgggg                                                            >  2:546249/1‑150 (MQ=255)                                                                                         aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAAAACCCCCCTTATTTTTTTCCATGGGTTGTTTTTTTCATCTTTTTAGTGCTTTTTTTTTTCTTTCCCCCTAACCCGTTCGGGGtt                                                          >  1:306992/1‑151 (MQ=255)                                                                                           tatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAAAAACCCCCTTTTTTTTTTCCGTGGGTTGTTTTTTTCCTCTTTCGAGTGCTTTTTTTTTTCTTCCCCCCTAAACCGTTTGGGGtt                                                          >  1:607663/1‑149 (MQ=255)                                                                                                tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATc                                                    <  2:823114/150‑1 (MQ=255)                                                                                                 gTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCg                                                  <  2:12680/151‑1 (MQ=255)                                                                                                   ccAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGtt                                                <  1:209505/151‑1 (MQ=255)                                                                                                      gTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATGAACACCCCCCTTTTTTTTTTCCGTGGGTCGTTTTTTTCCTCTTTTTAGTGGTTCTTTTTTTCTTTCACCCTAACCCGGTTGGGGTTCGCATCCCtt                                                >  1:860936/1‑148 (MQ=255)                                                                                                            agGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCg                                        <  2:533399/150‑1 (MQ=255)                                                                                                                              ttCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                      <  2:11437/150‑1 (MQ=255)                                                                                                                                                  tataCATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt  <  1:416184/150‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                     AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413589‑1413883

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: ‑