Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,576,077	0	C	A	42.5%	54.7 / 25.2	48	D515Y (GAT→TAT)	yddB	putative TonB‑dependent outer membrane receptor
Reads supporting (aligned to +/- strand):  ref base C (25/2);  new base A (0/20);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 2.37e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCAC  >  NC_000913/1575931‑1576212                                                                                                                                                      |                                                                                                                                         cgcAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCa                                                                                                                                         >  1:829061/1‑148 (MQ=255)   cAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAat                                                                                                                                    >  2:893981/1‑151 (MQ=255)     aTAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAatat                                                                                                                                  >  1:822996/1‑151 (MQ=255)       aaCGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑c                                                                                                                               <  2:309808/151‑1 (MQ=255)                aCCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCAt                                                                                                                        >  1:628655/1‑149 (MQ=255)                 ccGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGt                                                                                                                     >  1:172649/1‑151 (MQ=255)                  cGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGt                                                                                                                     >  2:420473/1‑150 (MQ=255)                     ttttCTGCTGCAATCCCATTGCCATTTCATCTTAAAAAGGCTTTTTAAAATCCTAATAACGCGTCAGTTTTTTTTTCCCTAA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAACCCCATAAAAAAAATATT‑CCCGCCATAGTAAc                                                                                                                  <  2:887932/150‑1 (MQ=255)                          tgctgcAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTtat                                                                                                            >  1:573604/1‑151 (MQ=255)                            ctgcAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTtata                                                                                                           >  2:462334/1‑150 (MQ=255)                             tgcAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAAc                                                                                                         >  2:498413/1‑151 (MQ=255)                             tgcAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAAc                                                                                                         >  1:445726/1‑151 (MQ=255)                                   cccATTGCAATTTCATCTTTATAGGGTTTTTTAAAATCCTGATACCGCGTCAGTTTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑TTATTGGGAATATCACGTAACCCCATATAAAGAATATT‑CCCGCCATAGTAACGGTTATaa                                                                                                          <  1:412517/144‑1 (MQ=255)                                              ttCATGTTTATAAGGTTTTTTCAATTCCTAATAACGCGTAAGATTTTTATTACCTAA‑T‑CCCGATCCCGTCCAG‑TTATTGCGAATATCACTTAACCCAATATCAAAAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCAtt                                                                                           <  2:484343/148‑1 (MQ=255)                                                  tCGTTATAAGGCGTTTCAAAACCCAAAAAACCGATAAGATTTTTATT‑CCTTA‑A‑TCCGGTTCCCCCCAGCCTTTTGGGAATATCACATAACCCAATACAAAGAATTTC‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAg                                                                                        <  2:553082/147‑1 (MQ=255)                                                   cGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTg                                                                                   >  1:217911/1‑151 (MQ=255)                                                       ataAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGAtt                                                                                >  1:425531/1‑150 (MQ=255)                                                       ataAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCAAGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGAtt                                                                                >  2:496789/1‑150 (MQ=255)                                                         aaggttttttAAAATCTTAATAACGCGTCAGATTTTTTTTCCCTAA‑T‑CCCGTTCCCGTCCAG‑CTTTTGCGAATATCCCGTAACCCCATATAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAg                                                                              <  1:79265/144‑1 (MQ=255)                                                           ggCTTTTTCAAATCCTGATAACGCGTCAGTTTTTTATTCCCTAA‑T‑CCCTATCCCCCCCAG‑CTATTGCAGATATCACGTAACCCCAAATAAATATTATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCaa                                                                           <  2:510063/151‑1 (MQ=255)                                                           ggCTTTTTAAAATCTTGATAACGCTTCATATTTTTTTTCCCTAA‑T‑CCCGATCCCGTCCAG‑CTGTGGCGAATATCCCTTACCCCCATAAAAAAATTATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCa                                                                            <  2:825151/150‑1 (MQ=255)                                                           ggCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCa                                                                            >  2:203460/1‑150 (MQ=255)                                                               ttttCAAATCCTGATAACGCGTCAGATTTTTTTTCCCTGA‑T‑CCCAATTCCGCCCAG‑CTTTTGCGAATATCACGTAACCCCAAAAAAAAAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCaaaa                                                                         <  1:850051/149‑1 (MQ=255)                                                               ttttAAAATCCTGATACCGCGTAAGTTTTTTTTTCCCTAA‑T‑CCCGTTTCCTCCCAG‑TTATTGCGGATATCACATAACCCCATATAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTATCaaa                                                                          <  2:880396/148‑1 (MQ=255)                                                                    aactcgtGATAACGCGTCAGATTTTTATTACCTGA‑T‑CCCGTTCCCGTCCAG‑CTATGGCGGTTATCACTAAACCCCATATAAAGAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATc                                                                    <  1:40282/143‑1 (MQ=255)                                                                          tGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCg                                                            >  1:319726/1‑151 (MQ=255)                                                                            aTAACGGTTCAGATTTTTTTTCCCTGA‑T‑CCCGATCCCGCCGAT‑TTTTGGCGAATATCAGGTAATCCTAAATAAAAAATATC‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTc                                                          <  2:282608/151‑1 (MQ=255)                                                                              accgggaaggatttttttTACCGGA‑T‑ACCGATTCCCGCCAG‑CTTTTCGGAATACCAGTTAACCCAATATAAAAAATTTC‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                        <  1:431281/139‑1 (MQ=255)                                                                               aCGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                        >  1:773467/1‑150 (MQ=255)                                                                               aCGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCAt                                                        >  2:316572/1‑150 (MQ=255)                                                                                 gcgTCAGTTTTTTATTCCCTGA‑T‑ACCGTTCCCGCCCAG‑CTATTGCGGATATCACTTAACCCCATATAAAAAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATaaa                                                     <  2:783443/151‑1 (MQ=255)                                                                                  gtgtagatTTTTTTTTCCTTATT‑ACCGTTCCCGTCCAG‑TTATTGTGTATTTTACGT‑ACCCCTTTTTAAAAATTTTACCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATa                                                       <  1:794150/145‑1 (MQ=255)                                                                                   gtcaattttttATTACC‑GA‑TCACCGTTCCCTTCCAG‑CTTTGGGGAAAATCACGAACCCCCAAAAAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATaaa                                                     <  2:398737/142‑1 (MQ=255)                                                                                      agatTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGAATATCACGTAACCCAATATAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAgcgc                                                 <  2:100837/150‑1 (MQ=255)                                                                                      agagTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGcgcg                                                >  2:276101/1‑151 (MQ=255)                                                                                         tttttttTCCCTGA‑T‑CCCGATCCCGCCCGT‑CTATTGGGAATATCACGAAACCCCATAAAAAAAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCggg                                              <  2:659648/149‑1 (MQ=255)                                                                                          ttttATTCCCTAA‑T‑CCCGATCCCGCCCAG‑CTATTGGGTATATCACTAAACCCAAAATAAAGAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAgcg                                                  <  2:530772/145‑1 (MQ=255)                                                                                              attaCCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGat                                         >  1:789685/1‑150 (MQ=255)                                                                                                    tGA‑T‑CCCGATCCCGTCAAG‑CTTTTGGGGATATCACATAACCCAATATAAAAAATTTT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATtgt                                    <  2:867110/149‑1 (MQ=255)                                                                                                     gA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGt                                 >  2:913808/1‑151 (MQ=255)                                                                                                        t‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGttt                               >  2:253325/1‑151 (MQ=255)                                                                                                        t‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGttt                               >  1:499190/1‑151 (MQ=255)                                                                                                            cGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGAc                            >  2:894497/1‑151 (MQ=255)                                                                                                             gATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGAc                            >  1:547928/1‑150 (MQ=255)                                                                                                             gATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGAc                            >  1:336549/1‑150 (MQ=255)                                                                                                                     ccAG‑CTATGGCGAATATCCCGTACTCCCATATAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGtt                    <  1:47064/150‑1 (MQ=255)                                                                                                                             ttGGGGATATCACTTACCCCCAAAAAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTgtcat               <  2:621181/148‑1 (MQ=255)                                                                                                                                        aCGTAACCCCATATAAAAAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCAc  <  2:346542/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                         CGCAATAACGTTCTTACCGATTTTCTGCTGCAATCCCATTGCCAGTTCATCGTTATAAGGCGTTTTCAAATCCTGATAACGCGTCAGAGTTTTATTACCTGA‑T‑ACCGATTCCGTCCAG‑CTATTGCGGATATCACGTAATCCCATATCAAGAATATT‑CCCGCCATAGTAACGGTTATAACCTGCTGTAATCATTGAGGTTTGATTAGCAAAAATATCCCATTCCGTCATAAAGCGCGGGGAGATATTGTGGTTTGACAGATAGTTGTCATAGTCATACCGCAC  >  NC_000913/1575931‑1576212

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: ‑