Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	52.3%	29.7 / 72.3	44	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (2/19);  new base T (23/0);  total (25/19)
Fisher's exact test for biased strand distribution p-value = 1.49e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-08

AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413589‑1413881                                                                                                                                                    |                                                                                                                                                   aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACa                                                                                                                                                <  2:430787/151‑1 (MQ=255) aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGG‑AAATTTTTAc                                                                                                                                                 >  1:223685/1‑150 (MQ=255)     ttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTtataaa                                                                                                                                                >  2:478612/1‑145 (MQ=255)         tttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGA‑ATTTTTTTACTTGGACAcc                                                                                                                                        >  2:712854/1‑151 (MQ=255)              gCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTc                                                                                                                                      <  1:197801/148‑1 (MQ=255)                tctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTAAATGaaaaacccc                                                                                                                                     >  1:190188/1‑140 (MQ=255)                 ctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTAAATGAAAACCTcc                                                                                                                                     >  1:69598/1‑146 (MQ=255)                   ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCatta                                                                                                                                 <  2:156199/148‑1 (MQ=255)                           gCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTACATGAAAACCTCCATTATTAttt                                                                                                                           >  1:147039/1‑146 (MQ=255)                            ccTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTg                                                                                                                     <  1:300081/151‑1 (MQ=255)                              tGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTATATTAAAACCCCCCTTTTTTTTTTCacttg                                                                                                                    >  1:465727/1‑146 (MQ=255)                               gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTgg                                                                                                                    <  2:679232/149‑1 (MQ=255)                                  tcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCg                                                                                                                <  1:55534/150‑1 (MQ=255)                                        ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AAATTTTTAAATGAAAAACCCCCTTATTATTTTCAGTGGTTCGtttttt                                                                                                          >  1:186158/1‑150 (MQ=255)                                         tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTACATGAAAACCCCCCTTTTTTTTTTCCGTGGGTTGtttttt                                                                                                          >  1:227098/1‑149 (MQ=255)                                          aCCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCa                                                                                                       <  2:23260/151‑1 (MQ=255)                                             tGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGA‑AATTTTTTTCATGAAAAACCACTTTATTTTTTTCAGTGGTTCGGTTTTTTCAtt                                                                                                     >  2:359883/1‑149 (MQ=255)                                                      tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTg                                                                                            <  1:502448/150‑1 (MQ=255)                                                         ttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑TATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGctt                                                                                         <  2:207261/150‑1 (MQ=255)                                                         ttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑CATTTTTTTCATAAAAAACCCCCTTATTATTTTCGATGGGTCGTTTTTTTCATCCTTcctaggcttt                                                                                        >  1:459147/1‑142 (MQ=255)                                                          tCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AAATTTTTACATTAACACCCCCCTTTTTTTTTTCACTGGGTTGGTTTTTTCATTTTTCTAGTGgttct                                                                                       >  1:542718/1‑151 (MQ=255)                                                            gCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCttt                                                                                     <  2:213362/151‑1 (MQ=255)                                                             cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCtttt                                                                                    <  1:136237/151‑1 (MQ=255)                                                               ttCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTTAACTAAAAACCCCCTTTATTTTTTCC‑GGGGTTTGTTTTTTTCATCTTTTTAGTGGttttttttt                                                                                  >  1:236572/1‑150 (MQ=255)                                                                tCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTAAATGAACACCCCCCTTTTTATTTTCCGTGGTTCGTTTTTTTCATCTTTTGAGTGCTTCttttt                                                                                   >  1:216228/1‑149 (MQ=255)                                                                 cTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTATATTAACACCTCCCTTTTTTTTTTTTGTGGGTTGTTTTTTTTATTTTTTTAGTGGtttttttttt                                                                                 >  2:436203/1‑148 (MQ=255)                                                                    aTTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACtt                                                                              <  2:69591/150‑1 (MQ=255)                                                                    aTTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGG‑AATTTTTTACATTAACACCTTCCTTTTTTTTTTTTGTGGGGGGTTTTTTTTTTCTTTCTATTGCtttttttt                                                                                   >  2:360128/1‑145 (MQ=255)                                                                     tttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATTTATAAACACCACCCTTTTTATTTTCACCGGTTTGCTTTTTTTATCTTTTCAGTGTTTCTTTTTTACTTc                                                                             >  1:154279/1‑150 (MQ=255)                                                                      ttCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTcc                                                                            <  1:314659/150‑1 (MQ=255)                                                                       tCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTcca                                                                           <  2:88423/150‑1 (MQ=255)                                                                           tAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTACATGAACACCCCCCTTATTTTTTTCCGTGGGTTGTTTTTTTCCTCTTTTTAGTGGTTTTTTTTTTCTTtcacc                                                                         >  1:462076/1‑148 (MQ=255)                                                                                   aTTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTc                                                              <  1:124336/151‑1 (MQ=255)                                                                                     tttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AAATTTTTAAATTAACACCCCCATTTTTTTTTTCCGTGGGTTGTTTTTTTCCTTTTTCCAGTGCTTCTTTTTTTCTTTCACCCTAAcccggt                                                               >  1:485141/1‑144 (MQ=255)                                                                                             tCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTTAATTAAAAACCCCCTTTTTTTTTTCCGTGGTTTGTTTTTTTCCTCTTTTTGGTGCTTTTTTTTTACTTCCCCCCTAAACCGGTCGGGGtt                                                        >  1:105623/1‑147 (MQ=255)                                                                                             tCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTATATGAAAACCTCCCTTTTTTTTTCCAGGGGGTTGGTTTTTTTATCTTTTCCGTGGTTTTTTTTTTTTTCCCCCCTAACCCGTTCTGGGtt                                                        >  2:392904/1‑147 (MQ=255)                                                                                                tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGC‑AATTTTTTTTAAGAACACCTCCCTTTTTTTTTTTCGTGGGTCGTTTTTTTCATTTTTCTAGGGGTTTTTTTTTTCTTTCACCCTAAACCGTTCCGGGTTTGCATc                                                  >  2:703693/1‑150 (MQ=255)                                                                                                        tagtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTTTAAATGGAAACCACCCTTATTATTTTCTGTGAGTTGTTTTTTTCATTTTTTGCTGGGTTCTTTTTTACTTCCCCCATAAACCGGTCGGGGTTTGCATTCGTTaaa                                           >  1:637075/1‑147 (MQ=255)                                                                                                         agtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACt                                         <  2:373071/150‑1 (MQ=255)                                                                                                                        ttccttTTCAATAGTGGCGGT‑AAATTTTTACATTAAAACCTCCCTTATTATTTTCAGTGGTTATTTTTTTTCATTTTTCTCGTTCTTCTTTTTTACTTTCCCCCTAACCAGTTTGGGTTTTGCATCCCTTTCACTTTTCCCTGTAata                            >  2:339292/1‑148 (MQ=255)                                                                                                                          ccttTTCAATAGTGGCGGT‑AATTTTTTTCATTAAAACCCCCCTTTTTTTTTTTTTTGGTTTGTTTTTTTCATCTTTTCCGTGGTTTTTTTTTTCTTTCCCCATAAACGGGTCGGGGGTTGCCTCCCTTATACTTCCCTCCGGAatattc                         >  1:661556/1‑147 (MQ=255)                                                                                                                               tCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAAt                   <  1:548774/150‑1 (MQ=255)                                                                                                                                    aGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCtt              <  1:430768/150‑1 (MQ=255)                                                                                                                                       ggCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCa           <  2:223662/150‑1 (MQ=255)                                                                                                                                                 tttATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg  >  2:545768/1‑150 (MQ=255)                                                                                                                                                    |                                                                                                                                                   AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGT‑AATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413589‑1413881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑