Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	51.8%	14.5 / 42.5	27	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (2/11);  new base T (14/0);  total (16/11)
Fisher's exact test for biased strand distribution p-value = 5.98e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.03e-05

GTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATG  >  NC_000913/1413590‑1413884                                                                                                                                                  |                                                                                                                                                       gTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTC‑TTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATg                                                                                                                                                  <  2:48575/151‑1 (MQ=255)      aCTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAac                                                                                                                                               <  2:498445/150‑1 (MQ=255)          tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCt                                                                                                                                           <  2:544643/150‑1 (MQ=255)            tGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAacaaccc                                                                                                                                          >  1:506277/1‑145 (MQ=255)                ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATAAatacacccc                                                                                                                                        >  1:417491/1‑142 (MQ=255)                    ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAAAGAAAACCCCCcttattttt                                                                                                                                >  2:309283/1‑151 (MQ=255)                    ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattattatt                                                                                                                                <  1:327141/151‑1 (MQ=255)                       aaCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATTAAAACCCCCCTtttttttt                                                                                                                               >  2:313891/1‑149 (MQ=255)                           ccTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATTAACACCTCCCTTATTTTTTTCAGT‑g                                                                                                                        >  2:473456/1‑151 (MQ=255)                              gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑gc                                                                                                                       <  1:99001/149‑2 (MQ=255)                                             gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCt                                                                                                       <  2:448004/150‑1 (MQ=255)                                                   aTTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTAATTAAAACCTCCCTTTTTTTTTTTAGT‑GGTTTGTTTTTTTCATtttt                                                                                                     >  1:189941/1‑146 (MQ=255)                                                           gCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGAAAATTTTTTTAAAAACACCCCCCTTTTTATTTTCTGT‑GGTTCGGTTTTTTCATCTTTTTAGGGCTTCttt                                                                                        >  2:42162/1‑151 (MQ=255)                                                                  gATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCa                                                                                    <  1:383512/148‑1 (MQ=255)                                                                       cGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAAAACCTCCCTTATTTTTTTCAGTGGGTTGGTTTTTTCC‑TTTTTTGTGTGGttttttttttctttcccc                                                                            >  2:271241/1‑141 (MQ=255)                                                                                     ttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCgg                                                               <  1:188747/150‑1 (MQ=255)                                                                                      tGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATATCTTAAAACCCCCATTATTTTTTTCCGT‑GGGTTGTTTTTTTCTTCTTTTTAGTGCTTTTTTTTTTATTTTACCATAACCAGTTccg                                                               >  1:389426/1‑147 (MQ=255)                                                                                        aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATGGAGAACTCCACTTTTTTTTTTTTT‑GGTTTGGTTATTTTATCTTTTTTGTGCTTTTTTTTTTCTTCCACCATAAACCGGTCggg                                                              >  1:324935/1‑148 (MQ=255)                                                                                         atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAACACCCCCCCTTTTTTTTTTATT‑GGTTTGTTTTTTTCATATTTTTAGGGCTTTTTTTTTTCTTTCCCCATTACCCGGTCGGGGtt                                                           >  1:126071/1‑150 (MQ=255)                                                                                             cTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAACACCTCCCTTATTATTTTCCGT‑GGTTCGGTTTTTTCATCTTTCTAGTGGTTCTTTTTTACTTTCCCCATAAACCGTTCGGGGTTTGCAt                                                      >  2:273656/1‑151 (MQ=255)                                                                                                        agtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGAAAAACCCCCTTTTTTTTTTCATT‑GGGTTGTTTTTTTTTTCTTTTTAGTGCTTCTTTTTTTCTTTCACCCTAAACGGGTCGGGGTTTGCCTCCGTTTTACtt                                           >  1:103968/1‑151 (MQ=255)                                                                                                          tagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTAAATAAAAAACCCCCTTTTTTTTTTCAGT‑GGGTCGTTTTTTTCATCTTTTTAGTGGTTTTTTTTTACTTTCACCATAAACGGGTTGGGGGTCGCATCCGtt                                                 >  2:117812/1‑143 (MQ=255)                                                                                                                      cttccttTTCAATAGTGGCGGTAATTTTTTACATTAACACCCCCCTTATTTTTTTCAGT‑GGGTCGTTTTTTTCATCTTTTGTGTGCTTTTTTTTTTCTTCCCCCATAAACCGTTCGGGGTTTGCCTCCCTTTCAcctccctccggaa                                 >  2:208178/1‑142 (MQ=255)                                                                                                                            tttCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGa                         <  2:423074/149‑1 (MQ=255)                                                                                                                                        cGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCg           <  2:82190/151‑1 (MQ=255)                                                                                                                                            aaTTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTAc       >  2:282710/1‑151 (MQ=255)                                                                                                                                             aTTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACt      <  1:177954/151‑1 (MQ=255)                                                                                                                                                  ataCATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg  <  2:207782/150‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                       GTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATG  >  NC_000913/1413590‑1413884

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: ‑