Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,415,806	0	G	T	43.6%	63.5 / 12.8	39	N527K (AAC→AAA)	recE	Rac prophage; exonuclease VIII, 5' to 3' specific dsDNA exonuclease
Reads supporting (aligned to +/- strand):  ref base G (20/2);  new base T (1/16);  total (21/18)
Fisher's exact test for biased strand distribution p-value = 6.33e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGGATCGCTGCCAGCATTCTCATTGTGCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTGGATCC  >  NC_000913/1415661‑1415945                                                                                                                                                     |                                                                                                                                            gCGGATCGCTGCCAGCATTCTCATTGTGCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTAt                                                                                                                                         <  1:244995/150‑1 (MQ=255)        gCTGCCAGCATTCTCATTGTGCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGcc                                                                                                                                  >  2:304699/1‑150 (MQ=255)                       aTTGTGCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGc                                                                                                                   >  2:253825/1‑150 (MQ=255)                         tgtgCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCAtt                                                                                                                >  1:387183/1‑151 (MQ=255)                                   ttCAGCCCCTTTCCTTTTCCCCCGA‑TTCTTTTTCTTAACCTCCACCCGCTCCCTCTCCATCAAATGTTCCCTGGTTTGTTCCGCCGCCCCCCCCCGCCCCAC‑GGCGGGGCAATTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTa                                                                                                        <  2:266022/150‑1 (MQ=255)                                   ttCAGCCCC‑TTCCATTCCCCCCGG‑ATCTTTTTCCTTAGCTCCACCCTCCCTCTCTTCATCGAATGTTCCCTGGTATGTTGCGTCCCCCACCCCCGCCCCACAGTCGGGGC‑AGTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTAt                                                                                                       <  1:94228/150‑1 (MQ=255)                                   ttCAGCCCC‑TCCCTTTCCCCCCGA‑ATCTTTTTCCTTAGCTCCACCCGGCCCCTCTTCATCGATTGTTTCCTGTTTTTTTGCGCCCCCCCCCCCCGCCCCACAGTCGGGGC‑ATTTCCCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTa                                                                                                        <  1:39995/149‑1 (MQ=255)                                        cgcC‑TTCCTTTCCCCCCGG‑ATTTTTTCCTTTGGCTCCACCCCGCCCCTCTTCATCGATTGTTCCCGGGTTTGTGGCGCCGCCCACCCCCCCACCACGGAGGGGGT‑TTTCACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCg                                                                                                  <  2:107360/150‑1 (MQ=255)                                                  tttCCTGCGA‑ATCTTTTCCCTGAGCTCCACCCGGTCTCCTTTCTTGGATTGTTTCCGGGTAGGTGGCGCCCCCCACCCCGGCCCAAGGGGGGGGGC‑ATTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCgg                                                                                                 <  2:286685/142‑1 (MQ=255)                                                   ttCCCCCGGTATCTTTTTCCTTAGCTCCACCCTGCCTCTCTCCAGCAATTGTTTCCTGTTTTTTGGGCCCGCCCGCCCCCGCCCCACAG‑CGGGGCTTTTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCg                                                                                                  <  2:167343/141‑1 (MQ=255)                                                       tccGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCact                                                                                    >  1:190434/1‑150 (MQ=255)                                                                 ttttCCTTTGCCTCCCCCTCCCTCTCTTCACCGATTTTTTCCTGTTTTGTCCCCCCCCCCACCCCCGCCCCACGGTCAGGGC‑TTTTCTCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCa                                                                           <  2:520163/150‑1 (MQ=255)                                                                 ttttCCTTAGCTCCACCCTGCCTCTCTTCATCGATTTTTTCCTGTTATGTTGCGCCCCCCACCCCCGCCCCACAGTCGGGGC‑ATTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCa                                                                           <  1:429618/150‑1 (MQ=255)                                                                        tAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTTCGTCGCCCATCACCGCACCACAGTCTGGGC‑ATTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGTTTCCTGTTGCACTACTGGCTCAGGTTGAtt                                                                   >  2:237098/1‑151 (MQ=255)                                                                        tAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGAtt                                                                   >  1:85191/1‑151 (MQ=255)                                                                           ctccaccctccctctctCCATCAATTGTTTCCTGGTATGTTGCGCCCCCCCCCCCCGCCCCACGGTCGGGGC‑ATTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCa                                                                 <  2:476141/139‑1 (MQ=255)                                                                            ttCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCat                                                                >  1:436522/1‑150 (MQ=255)                                                                            ttCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCat                                                                >  2:350576/1‑150 (MQ=255)                                                                                  cTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTggg                                                         >  1:650920/1‑151 (MQ=255)                                                                                       tctctTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGt                                                    >  1:513747/1‑151 (MQ=255)                                                                                              atagAATGTTTCCTGGTTTGTTGCGCCCCCCACCCCCGCCCCACAGTCAGGGC‑ATTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTc                                              <  1:549050/147‑1 (MQ=255)                                                                                                  atttttccttgttttGTTGCGCCCCCCCCCCCCCCCCCACGGTGGGGGC‑ATTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGtttttt                                               <  1:3651/131‑1 (MQ=255)                                                                                                        tCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTctggct                                   >  2:302370/1‑151 (MQ=255)                                                                                                        tCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTT‑CGTTTctggct                                   >  2:690204/1‑150 (MQ=255)                                                                                                         ccTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTctggctg                                  >  2:188004/1‑151 (MQ=255)                                                                                                                 gTTGCGTCCCCCACCCCCCCCCCACGTTGGGGGC‑GTTTCCCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTg                            <  1:373641/149‑1 (MQ=255)                                                                                                                     cGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTacac                      >  1:407271/1‑151 (MQ=255)                                                                                                                     cGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTaca                       >  2:112689/1‑150 (MQ=255)                                                                                                                        cccccctcccccccccacGGTCGGGGC‑TTTTCCCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTAcacaca                   <  2:468721/137‑1 (MQ=255)                                                                                                                        cccccaccccccccccacAGTCGGGGC‑ATTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTac                        <  1:625616/132‑1 (MQ=255)                                                                                                                           ccATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATc                >  1:84374/1‑151 (MQ=255)                                                                                                                                aCCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTctg                                      >  1:274797/1‑124 (MQ=255)                                                                                                                                  cGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTc         >  2:552823/1‑151 (MQ=255)                                                                                                                                    caccacAGTGGGGGA‑ATTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCt        <  1:476012/150‑1 (MQ=255)                                                                                                                                    caccacAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTg       >  2:412220/1‑151 (MQ=255)                                                                                                                                      ccacAGTCGGGGC‑ATTTACCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTg       <  1:67691/149‑1 (MQ=255)                                                                                                                                       cacaGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTGGAt    >  1:529095/1‑151 (MQ=255)                                                                                                                                         caGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTGGATcc  >  1:228823/1‑151 (MQ=255)                                                                                                                                             cAGGGC‑ATTTCTCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTGGATc   <  1:176940/146‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                            GCGGATCGCTGCCAGCATTCTCATTGTGCGGATGTTCAGCGCC‑TTCCATTTCCTCCGG‑ATCATTTTCCTTAGCTTCAACCTGACTCTCTTCATCGAATGTTTCCTGGTATGTTGCGTCGCCCATCACCGCACCACAGTCAGGGC‑AGTTATCCCCGCCAGTCTGGCCGCAGGCATTGCAGGCTATTTCCGGTTCCTGTTGCACTACTGGCTCAGGTTGATTCATATCTGGGCTGGTTTTTTCCGTTTCTGGCTGGTTCTGGTACACACAATCGCGAGTCTGGATCC  >  NC_000913/1415661‑1415945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑