Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	46.5%	33.5 / 36.5	43	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (6/17);  new base T (20/0);  total (26/17)
Fisher's exact test for biased strand distribution p-value = 2.42e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413589‑1413883                                                                                                                                                     |                                                                                                                                                        aGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGAGCCACAATCCTTTCCAATAGTGGCGG‑TA‑ATTTTATACa                                                                                                                                                     <  1:819159/151‑1 (MQ=255)    tttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTtttata                                                                                                                                                     >  2:5183/1‑146 (MQ=255)    tttACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATg                                                                                                                                                   <  1:467146/150‑1 (MQ=255)     ttACTTTATGCTCTCAGGCAAGGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TT‑ATTTtttaatag                                                                                                                                                   >  1:488041/1‑145 (MQ=255)       aCTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTTCATGaa                                                                                                                                                 >  1:372065/1‑149 (MQ=255)          ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TATATTTTTTACTTGacacc                                                                                                                                              >  2:326353/1‑146 (MQ=255)           tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCt                                                                                                                                            <  1:441854/150‑1 (MQ=255)            cTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTACATAAACACCTcc                                                                                                                                          >  2:541177/1‑151 (MQ=255)              gCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCat                                                                                                                                        <  2:3339/151‑1 (MQ=255)               ctctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTATATTAacaacccc                                                                                                                                          >  2:11824/1‑143 (MQ=255)                tctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTATATTaaaaaccc                                                                                                                                           >  1:594771/1‑140 (MQ=255)                     ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCattattatt                                                                                                                                 <  2:271902/151‑1 (MQ=255)                          cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAg                                                                                                                            <  1:213764/151‑1 (MQ=255)                           gCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGt                                                                                                                           <  2:642540/151‑1 (MQ=255)                           gCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGt                                                                                                                           <  2:802274/151‑1 (MQ=255)                               gCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTTCATTAAAACCCCCCCTTTTTTTTTCAGT‑ggg                                                                                                                       >  1:548069/1‑149 (MQ=255)                                     tttttACCTGAGAGCATTTTTTCGCATTCTGCTTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTATATAAAAACCCTCACTTTTATTTTCATT‑ggagcggt                                                                                                                  >  2:669637/1‑143 (MQ=255)                                     tttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGtt                                                                                                                  <  2:685450/149‑1 (MQ=255)                                        ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTATATAAAAAACCCCACTTTTTTTTTCAAT‑GGGTTGTTTAttt                                                                                                             >  1:817133/1‑150 (MQ=255)                                        ttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTACATGAACACCCCCCCTTTTTTTTTCCGT‑GGTTTGttttttt                                                                                                             >  2:135720/1‑150 (MQ=255)                                             tGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑AATTTTTATAAAAAAACCACCATTTTTTTTTTCAGT‑GGGTCGTTTTTTTCAt                                                                                                          >  2:216163/1‑149 (MQ=255)                                               agagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTAAATGAACACCCCCCTTATTTTTTTCAGTGGGTTGGTTTTTTCC‑TCttt                                                                                                      >  2:47783/1‑151 (MQ=255)                                               agagCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCttt                                                                                                      <  1:484228/151‑1 (MQ=255)                                                     ttttttCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTA‑TTTTTTTACAT‑AACACCTCCCTTTTTTTTTTCAGT‑GGTTCTTTTTTTTCATCttt                                                                                                      >  2:148508/1‑145 (MQ=255)                                                            gCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCttt                                                                                         <  2:656989/151‑1 (MQ=255)                                                                 cTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGATA‑ATTTTTTTCTTTACAACCTCCTTTTTTTTTTTCA‑T‑GGGTCGTTTTTTTCCTTTTTTTGGTGCtttttttt                                                                                       >  2:97836/1‑148 (MQ=255)                                                                              tttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTTAATATAAAACTCCATTATTATTTTCAATGGGTTGGTTTTTTCC‑TCTTTTGCGGGCTTCTTTTTTTCTTTCA‑CCATaa                                                                        >  2:343453/1‑149 (MQ=255)                                                                                      ttGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCgg                                                              <  2:267075/150‑1 (MQ=255)                                                                                         aaTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑AATTTTTATAAAAAAACCCCCCTTATTATTTTCCGG‑TGTTTGTTTTTTTCCTCTTTTTCGTGGGTCTTTTTTACCTTCA‑CCATAAAC‑AGTTCggg                                                             >  2:624498/1‑148 (MQ=255)                                                                                          atatCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑AATTTTTAAATTAAAACCCCCCCTTTTTTTTTCACT‑GGGTCGTTTTTTTCTTCTTTTTAGTGGTTCTTTTTTTCTTTTA‑CCCTAAAC‑CGTTCGGGGttt                                                         >  1:481708/1‑150 (MQ=255)                                                                                                tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTACATGAACACCTCCCCCATTTTTTTCCTT‑GGTTTGTTTTTTCTCTCTTTTTCGTGCTTCTTTTTTTTTTCCA‑CCCTAACC‑CGTTCGGGGTTCtcctcc                                                   >  1:464719/1‑151 (MQ=255)                                                                                                tGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCAt                                                     <  2:390882/149‑1 (MQ=255)                                                                                                    cAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑AATTTTTATATTAACAACTCCCTTTTTTTTTTTCAT‑GGTTCGTTTTTTTTATCTTTTTTGTGGTTCTTTTTTTCTTCCA‑CCAAAACC‑GGTTTGGGGTTCGCCTCCCttt                                               >  1:365873/1‑150 (MQ=255)                                                                                                             ggAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTTTTCATGAAAACCCCCCCTTTTTTTTTTAAT‑GGGTCGGTTTTTTCTTCTTTCGAGGGCCTTTTTTTTTCTTTCACCCAAAACC‑GTTTCGGGtttgcctccctttt                                               >  1:590249/1‑132 (MQ=255)                                                                                                              gAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTc                                     <  2:791752/151‑1 (MQ=255)                                                                                                               aGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑AATTTTTACATTAACAACCCCCCTATTATTTTCAGT‑GGGTTGGTTTTTTCATCTTTTTAGTGCTTTTTTTTTACTTCCA‑CCATAACCGGGTTCGGG‑TTCGCATCCCTTTCACTTCGc                                       >  2:59572/1‑148 (MQ=255)                                                                                                                  gCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGt                                  <  2:372103/150‑1 (MQ=255)                                                                                                                         ttcttTTCAATAGTGGCTG‑TA‑ATTTTATACATGTACACCTCCATTATTATTACCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATCACT‑GGTTCCGGCTTCGCATCTGTTACACTTCGCTCGGTCATATca                           <  1:51671/148‑2 (MQ=255)                                                                                                                               tCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAAt                     <  2:55102/150‑1 (MQ=255)                                                                                                                                      tGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTc              >  2:687094/1‑150 (MQ=255)                                                                                                                                      tGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGGTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTc              >  1:120490/1‑150 (MQ=255)                                                                                                                                                 ttttATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg    >  2:224811/1‑151 (MQ=255)                                                                                                                                                 ttttATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg    >  2:89883/1‑151 (MQ=255)                                                                                                                                                  tttATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg    >  1:134819/1‑150 (MQ=255)                                                                                                                                                   ttATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt  >  2:629403/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                        AGTTTTACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGG‑TA‑ATTTTATACATGAACACCTCCATTATTATTTCCAGT‑GGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCA‑CCATAACC‑GGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAT  >  NC_000913/1413589‑1413883

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: ‑