Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	48.8%	36.5 / 31.1	41	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 (20/0);  total (22/19)
Fisher's exact test for biased strand distribution p-value = 9.40e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413593‑1413881                                                                                                                                               |                                                                                                                                                     ttACTTTCAGCTCTCTGGAAACGGCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGCTTTTGAATATCTTGTCCCGTTAGTAGGAGTCCCACTTTCCTTTTCAATAGTGGCGGGCATTTTTTA‑ctt                                                                                                                                                >  1:441558/1‑146 (MQ=255)  tACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑AATTaa                                                                                                                                             >  2:946407/1‑150 (MQ=255)    cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTGATTTTTTA‑TATaaaaa                                                                                                                                           >  2:889208/1‑148 (MQ=255)      ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAaca‑c                                                                                                                                         <  2:755505/149‑1 (MQ=255)       tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTT‑TATTAACA‑cc                                                                                                                                        >  1:539114/1‑149 (MQ=255)          gCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCa                                                                                                                                    <  2:794166/150‑1 (MQ=255)           ctctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAAct‑cctc                                                                                                                                      <  1:392409/147‑1 (MQ=255)               ctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCattat                                                                                                                                <  2:955695/149‑1 (MQ=255)                     aCGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCa                                                                                                                        <  1:606455/151‑1 (MQ=255)                       gCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTT‑CATTAACA‑CCCCCATTATTTTTTTCAGt                                                                                                                      >  2:895449/1‑151 (MQ=255)                           gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGtt                                                                                                                  <  1:961548/151‑1 (MQ=255)                            cttcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTATAATAAAAA‑CCCCCA‑TATTAttttctttgggt                                                                                                                  >  2:26640/1‑141 (MQ=255)                               cttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGGAATTTTTTT‑AATTAACA‑CCTCCCTTTTTTTTTTCCGTtgtttgtt                                                                                                              >  1:163885/1‑151 (MQ=255)                                   tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTT‑TATGAACA‑CCTCCCTTATTTTTTTCAGTGGGTTGtttttt                                                                                                          >  2:521044/1‑151 (MQ=255)                                    ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTAtt                                                                                                          <  1:317229/150‑1 (MQ=255)                                     tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑CATGAAAA‑CCCCCCTTATTTTTTTCCGTGGGTTGtttttt                                                                                                          >  2:319130/1‑149 (MQ=255)                                            gagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTc                                                                                                 <  2:492499/151‑1 (MQ=255)                                             agCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑TATGAAAA‑CCCCCCTTATTTTTTTCCGTGGGTTGTTTTTTTCCTCttt                                                                                                  >  2:796686/1‑149 (MQ=255)                                                  tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑CATGAAAA‑CCCCCCTTTTTTTTTTCCATGGGTTGTTTTTTTCATCttttttgtg                                                                                            >  2:810014/1‑144 (MQ=255)                                                  tttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTA‑CAAGAAAA‑ACCCCCTTATTTTTTTCTCTGGTTCGTTTTTTTCATCttt                                                                                                  >  2:153014/1‑144 (MQ=255)                                                   ttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑AAATAACA‑CCCCCCTTTTTTTTTTTTGTGGGTCGTTTTTTTTTTCTTTCTTGTGct                                                                                          >  1:82222/1‑151 (MQ=255)                                                    tttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑AATTAAAA‑ACCCCCTTATTATTTTCAGTGGGTCGTTTTTTTCATCTTTTGAGGGctt                                                                                         >  2:885582/1‑151 (MQ=255)                                                      tCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑AAATAACA‑ACCCCACTATTTTTTTCAGTGGGTTGTTTTTTTCTTCTTTTGTGTGgtttt                                                                                       >  2:346565/1‑149 (MQ=255)                                                       cGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑CAATAACA‑CCCCCCTTATTATTTTTTGTGGGTTGTTTTTTTCCTCTTTCTATTGgttctt                                                                                      >  2:549882/1‑151 (MQ=255)                                                       cGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑AAAGATAA‑ACCCCCTTTTTATTTTCTGTGGTTCGTTTTTTTTTTCTTTTGAGGGcttctt                                                                                      >  1:310487/1‑151 (MQ=255)                                                       cGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGcttct                                                                                       <  1:139964/150‑1 (MQ=255)                                                             cTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑CATGAACA‑ACTCCCATTTTTTTTTTAATGGGTCGTTTTTTTCCTCTTTTTAGTGCTTCttttt                                                                                   >  1:878754/1‑148 (MQ=255)                                                                    cGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTccac                                                                          <  1:601883/150‑1 (MQ=255)                                                                      ttAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTA‑CAAGAAAA‑CCCCCCTTATTTTTTTCCGTGGGTTGTTTTTTTCCTCTTTTTAGTGGTTTTTTTTTTCTTccccc                                                                         >  2:262400/1‑149 (MQ=255)                                                                           ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAAcc                                                                   <  2:238371/150‑1 (MQ=255)                                                                           ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAAcc                                                                   <  2:906257/150‑1 (MQ=255)                                                                                      atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTc                                                       <  2:933723/151‑1 (MQ=255)                                                                                            tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTT‑AATTAACA‑CCCCCCTTTTTTTTTTCAGTGGGTCGTTTATTTTATCTTTTTGGTGCTTTTTTTTTTCTTCCACCCTTACCGGTTTGGGGTTTGcct                                                   >  1:450058/1‑147 (MQ=255)                                                                                                 aGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTac                                            <  2:502142/151‑1 (MQ=255)                                                                                                     agtagGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTT‑CAAAAACACCCCCCCTTTTTTTTTCCA‑TGGGTCGTTTTTTTCCTCTTTTCCGCGGTTCTTTTTTTTTTCCCCCCCAACCCGCTCGGGATTTGCCTCCgcttc                                            >  2:638997/1‑143 (MQ=255)                                                                                                              gCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGt                                <  2:37338/150‑1 (MQ=255)                                                                                                                         tttCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGaa                     <  1:57436/150‑1 (MQ=255)                                                                                                                           tCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAAt                   <  1:26638/150‑1 (MQ=255)                                                                                                                            cAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATgg                 <  2:443988/151‑1 (MQ=255)                                                                                                                            cAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATg                  <  1:653864/150‑1 (MQ=255)                                                                                                                                            tttATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg  >  2:889211/1‑150 (MQ=255)                                                                                                                                               |                                                                                                                                                     TTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATA‑CATGAACA‑CCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTG  >  NC_000913/1413593‑1413881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑