Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	40.5%	48.9 / 20.1	37	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (2/20);  new base T (15/0);  total (17/20)
Fisher's exact test for biased strand distribution p-value = 1.45e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TATCAGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATG  >  NC_000913/1413585‑1413884                                                                                                                                                       |                                                                                                                                                         tATCAGTTTTACTTTCTG‑‑CTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTtat                                                                                                                                                         <  1:784829/150‑1 (MQ=255)     aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTtata                                                                                                                                                        <  1:125533/149‑1 (MQ=255)        tttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATg                                                                                                                                                    <  1:729646/150‑1 (MQ=255)           aCTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAGTTTATACATGAaca                                                                                                                                                <  2:213838/151‑1 (MQ=255)               tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTaaaa                                                                                                                                                >  1:559073/1‑145 (MQ=255)               tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCt                                                                                                                                             <  1:475096/150‑1 (MQ=255)                    tctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTTCATGAAAACCTCCctt                                                                                                                                        >  1:77064/1‑150 (MQ=255)                         ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattatta‑t                                                                                                                                  <  1:101877/150‑1 (MQ=255)                          gAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATTAAAAACCCCCTTAttt‑ttt                                                                                                                                >  1:620422/1‑151 (MQ=255)                              cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTATATGTACACCCCCATttttt‑tttt                                                                                                                               >  2:88634/1‑147 (MQ=255)                                ccTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTg                                                                                                                          <  2:586563/151‑1 (MQ=255)                                   gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTgg                                                                                                                         <  1:793067/149‑1 (MQ=255)                                           tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAACACCCCCCCTATTA‑TTTTCAGTGGGT‑CGtttttt                                                                                                              >  1:78227/1‑151 (MQ=255)                                            ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTAtt                                                                                                              <  2:372357/150‑1 (MQ=255)                                              aCCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTcc                                                                                                            <  1:67590/150‑1 (MQ=255)                                                  gagaGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCtt                                                                                                       <  1:356936/151‑1 (MQ=255)                                                         ttttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTATATTTATACATGAAAAACTCCATTATTT‑TTTCTCGTGGGT‑GTTTTTTTTCTTCttttttgt                                                                                                 >  2:246486/1‑145 (MQ=255)                                                                 cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCAAGAACACCTCCCTTATTA‑TTTTCCTTGGTT‑CGGTTTTTTtttctttctggttgttttttt                                                                                        >  2:59661/1‑138 (MQ=255)                                                                    tCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTAAATGAACACCTCCCTTTTTATTTTTCTAGGGTT‑CTTTTTTTCC‑TTTTTTGTGTGCTTC‑ttttt                                                                                      >  2:241713/1‑149 (MQ=255)                                                                               tAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATGGACACCCCCCCTATTT‑TTTTTAGCGGGT‑TGTTTTTTTCATCTTTTTCGGGGTTC‑ttttttatcttcacc                                                                            >  2:188441/1‑138 (MQ=255)                                                                                aGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATTAAAACCCCCCTTATTA‑TTTTCAATGGTT‑TGTTTTTTTCATCTTTTGAGTGCTTT‑TTTTTTTCTTccacc                                                                            >  1:271480/1‑147 (MQ=255)                                                                                aGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATa                                                                         <  2:90281/150‑1 (MQ=255)                                                                                   ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAAcc                                                                      <  1:233874/150‑1 (MQ=255)                                                                                     aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGt                                                                   <  1:548379/151‑1 (MQ=255)                                                                                          ttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATGAACACCCCCCTTATTT‑TTTTCAGTGGGT‑TGTTTTTTTCATCTTTTGTGTGCTTC‑TTTTTTTCTTCCACCCTAACCCGTTCggg                                                              >  1:538444/1‑151 (MQ=255)                                                                                          ttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATGAAAACCCCCCATATTT‑TTTTCCGTGGGT‑TGTTTTTTTCATCTTTTGAGGGGTTC‑TTTTTTTCTTTCCCCCTAAACCGGTCggg                                                              >  1:675345/1‑151 (MQ=255)                                                                                            gAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAAAACCTCCCTTATTT‑TTTTTTGTGGGT‑TGTTTTTTTCATTTTTTGAGCGCTTT‑TTTTTTTCTTTCCCCCTAACCGGt                                                                   >  2:358343/1‑144 (MQ=255)                                                                                             aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGAtt                                                           <  1:514420/151‑1 (MQ=255)                                                                                                  cTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTAAAATAACACACCCCTTTTTA‑TTTTTATCGGGG‑TGGTTATTTCCTCCTTCCAGTGGTTCTTTTTTCTCTTCCCCCTAAACCCCTTCggggtc                                                           >  2:357412/1‑144 (MQ=255)                                                                                                    tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATc                                                     <  1:358458/150‑1 (MQ=255)                                                                                                      tCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAACACCCCCCTTTTTA‑TTTTTCGTGGTT‑CGTTTATTTTATTTTTTGAGTGCTTT‑TTTTTTACTTTCACCCTTACCCGTTCTGGGttttcat                                                      >  2:120209/1‑142 (MQ=255)                                                                                                        cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGACATTTTTTAAATGTAAACAACCCCTTTTT‑TTTTCAGTGGTTGTTTTTTTTCCTTTTTTTGTGT‑CGTT‑TTTTTTTCTTCCCCCATAAACGGGTCTGGATTCCCATcccct                                                 >  1:790930/1‑147 (MQ=255)                                                                                                                          ccttccttTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAatat                              <  1:582896/151‑1 (MQ=255)                                                                                                                                  ttCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                       <  1:600105/150‑1 (MQ=255)                                                                                                                                  ttCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaaa                       <  2:32542/150‑1 (MQ=255)                                                                                                                                               gTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGtt         >  1:203824/1‑151 (MQ=255)                                                                                                                                                 aaTTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTa        <  1:434638/150‑1 (MQ=255)                                                                                                                                                 aaTTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTa        <  1:111522/150‑1 (MQ=255)                                                                                                                                                  aTTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGGTTC‑TTTTTCACTTCCGCCATAACCGGTTCGGGATTCGCATCCGTTACACTGCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTAc       <  2:427866/150‑1 (MQ=255)                                                                                                                                                       ataCATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATg  <  1:11816/150‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                                         TATCAGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTA‑TTTCCAGTGGTT‑CGTTTATTCCATCTTTCGAGTGCTTC‑TTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATG  >  NC_000913/1413585‑1413884

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑