Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	56.0%	12.9 / 34.4	25	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (1/10);  new base T (14/0);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 3.37e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.44e-05

TTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGG  >  NC_000913/1413591‑1413866                                                                                                                                                 |                                                                                                                                     ttttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATAc                                                                                                                                   <  1:32973/148‑1 (MQ=255) ttttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACa                                                                                                                                  <  2:219735/149‑1 (MQ=255)     aCTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTCATTaaaa                                                                                                                            >  2:295458/1‑149 (MQ=255)       tttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTtttattagaaaac                                                                                                                           >  2:447928/1‑141 (MQ=255)               ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAAAACCTCCctttt                                                                                                                  >  1:443286/1‑149 (MQ=255)                 ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATTAACACCCCCctttttt                                                                                                                >  2:81152/1‑150 (MQ=255)                 ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattatta                                                                                                                <  1:501697/151‑1 (MQ=255)                      aaCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTcc                                                                                                           <  2:458703/151‑1 (MQ=255)                         gCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAACACCTCCCTTATTTTTTTCAGt                                                                                                        >  1:238387/1‑151 (MQ=255)                              cttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTc                                                                                                   <  2:275767/151‑1 (MQ=255)                                       tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTcc                                                                                          <  2:248315/151‑1 (MQ=255)                                                    tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGc                                                                             <  2:290847/151‑1 (MQ=255)                                                                            tttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑cc                                                    <  1:203130/151‑1 (MQ=255)                                                                               aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAAAACCCCCATTTTTTTTTTCAGTGGGTTGGTTTTTTCATTTTTTTAGGGCTTTTTTTTTTCTTTCCCCATaaaccgt                                                  >  2:119451/1‑146 (MQ=255)                                                                                          atCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAACACCCCCCTTTTTATTTTCAGTGGGTCGTTTTTTTCCTCTTTTTAGTGCTTCTTTTTTACTTCCACCATAACCCGGTTGGGGtttg                                        >  1:328482/1‑149 (MQ=255)                                                                                          atCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACACCCCCCTTATTTTTTCCCGTGGTTCGTTTATTTCATCTTTTGAGTGCTTCTTTTTTACTTCCACCATAA‑CCGGTTTGGGGtttg                                       >  1:414212/1‑148 (MQ=255)                                                                                            cTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑CCGGTTCGGGATTCGCAt                                    <  2:538517/151‑1 (MQ=255)                                                                                               gTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGTGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑CCGGTTCGGGATTCGCATCCg                                 >  1:251209/1‑151 (MQ=255)                                                                                               gTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACACCCCCCTTATTTTTTTCAATGGGTCGTTTTTTTCATCTTTTGAGTGGTTTTTTTTTACTTTCCCCATAA‑CCCGTTTGGGGTTTGCCTcc                                  >  1:397433/1‑150 (MQ=255)                                                                                                   aGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAAAGAAAACCCCCACTTTTTTTTTCCGTGGGTCGTTTTTTTTATCTTTTTAGTGCTTCTTTTTTTCTTCCCCCCTAA‑ACGGTTTGGGATTTGCATCCGttt                              >  2:130739/1‑149 (MQ=255)                                                                                                    gTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGGAAACCCCCCTTTTTTTTTTCAAGGGGTCGTTTTTTTCATCTTTCTAGTGCTTCTTTTTTTCTTCCCCCATAA‑ACGGTTTGGGGTTCGCATCCCTTaca                            >  2:293931/1‑151 (MQ=255)                                                                                                    gTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAACACCCCCCTTTTTTTTTTCAGTGGGTCGTTTTTTTTATCTTTTGAGTGCTTTTTTTTTTCTTTCCCCATAA‑CCCGTTCGGGGTTTGCCTCCGTTtca                            >  2:610428/1‑151 (MQ=255)                                                                                                        gtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAAAACCCCCCTTTTTTTTTTCCGTGGGTCGTTTTTTTCATCTTTTTAGGGGTTCTTTTTTTCTTTCACCCTAA‑CCCGTTCGGGGTTTGCATCCGTTACACtt                         >  2:570789/1‑150 (MQ=255)                                                                                                                 ccACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTaa               <  1:353396/151‑1 (MQ=255)                                                                                                                           tttCAATAGTGGCGGTAATTTTTTAAATGAACACCTCCCTTATTATTTTCAGTGGGTCGTTTTTTTCATTTTTTGAGTGCTTCTTTTTTTCTTTCACCCTAA‑ACGGTTCGGGGTTCGCATCCGTTTCACTTTCCTCCGTAATATTCTGaaa     >  2:170159/1‑151 (MQ=255)                                                                                                                              cAATAGTGGCGGTAATTTTTTACATGAAAACCCCCATTATTATTTTCAGTGGGTCGTTTATTTCATCTTTTGAGTGCCTCTTTTTTTATTTCACCATAA‑ACGGGTCGGGGTTTGCATCCGTTACACTTCGCTCGGGAATAACCTGAAATgg  >  2:21232/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                     TTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAA‑CCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGG  >  NC_000913/1413591‑1413866

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑