Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	46.0%	76.9 / 10.6	51	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (23/4);  new base C (0/23);  total (23/28)
Fisher's exact test for biased strand distribution p-value = 1.68e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376359‑1376652                                                                                                                                                    |                                                                                                                                                    tACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACAcc                                                                                                                                                   <  1:390958/149‑1 (MQ=255)  aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                >  1:59863/1‑151 (MQ=255)  aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                >  1:587332/1‑151 (MQ=255)  aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                >  1:500505/1‑151 (MQ=255)     gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                             <  2:587589/151‑1 (MQ=255)             ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccg                                                                                                                                     <  2:67043/151‑1 (MQ=255)                  ccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGtt                                                                                                                                >  1:39432/1‑151 (MQ=255)                    gcgTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTAc                                                                                                                              >  2:631101/1‑151 (MQ=255)                       tAGCCTGGACGGCGGCCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACAGCTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTATAtc                                                                                                                           >  2:132203/1‑151 (MQ=255)                          ccTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtc                                                                                                                        >  2:99786/1‑151 (MQ=255)                          ccTGGACGGCGACCGCAAAAGGGGGAGTGTTCCCCTGCGCGTACGGAAACGGGTCGCCGCGCGTCCCGGACCCGGGGTTTATCTCGACCCTTAAAA‑CCGCTATAAGGATCATATGATCACCCCCCCCGCCGATGCCCGCCGTTACAtcgtc                                                                                                                        <  1:562075/151‑1 (MQ=255)                             ggccGGCGCCCGCAAATGGGGGGGTGATCCCCGGCGCTTACGGGACCAGGTCGCCGCGCGCACCGGACCCGTGGTTTACCCCGACCCGTTAAC‑CCCCTATCAGGATTAAATAATAACCCCCCCCCCCGATGCCCGCCGTTACAtcgtc                                                                                                                        <  2:490608/145‑1 (MQ=255)                             ggccGGCGCCCGAAAAATGGTGAGTGATCCCCTGCGCGTACGGGACCGGGTCGCCGCGCGTCCCGGACCGGTGGTTTATCTCGACCCTTTAAC‑CCGCTATCAGGATCATATGATCACCCCCCCCGCCGATGCCCGCCGTTACAtcgtc                                                                                                                        <  1:50682/145‑1 (MQ=255)                                 ggCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCCGTGGTGTATCTCGAACCGTTAAC‑CCGCTATCAGGATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                                 <  1:656527/151‑1 (MQ=255)                                      ccGAAAAAGGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCCCCGCGCGTACCGAAACCGTGGTGTATCCCGAACCTTAAAC‑CCCCTATCAGGATCATATGATCAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATc                                                                                                              <  1:278793/149‑1 (MQ=255)                                        gCAAAATGGGGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                            >  2:334866/1‑149 (MQ=255)                                          aaaaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                        >  2:636484/1‑151 (MQ=255)                                               ggggggtgaTCCCCTGCGCGTACTGGAACGGGTCGCCGCGCGTACCGGACCCGGGTTGTATCTCGACCCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                                     <  1:110498/144‑1 (MQ=255)                                                      gttccccGGCGCTTATTGGAACGGGTCCCCGCGCATTCCGCACCCGTGGTATATCCCGACCCGTAAAA‑CCGCTACAAGGATAATATGATAAACCCCCTCGCGAACGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTa                                                                                            <  1:103253/147‑1 (MQ=255)                                                        ttCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                          >  1:461636/1‑151 (MQ=255)                                                          ccgtGCGCTCACTGAAGCAGGTCGCCGCGCCT‑CCAGGACCGTGGGTTTACACCTACCATTAAACCCGCTCTAAGAATAATATAATCATCCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAgatgat                                                                                           <  2:534424/145‑1 (MQ=255)                                                           ccTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                       >  1:948198/1‑151 (MQ=255)                                                             tGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                      >  2:454655/1‑150 (MQ=255)                                                              gcgcGTACGGAACCAGGCCGCGGCGCGTCCCGGAACGGTGTTGTATCCCGAACCGTAAAA‑CCACTATCGGGATAATATAACCACCCCCCACGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                             <  2:974659/142‑1 (MQ=255)                                                                gcgTAGGGGAACAGGCCGCCGCGCGTACCGGACCCGTGGTTTATCTCAAACCGTAAAC‑CCCCTATCAGGATCATATGACCACCCCCCCCCCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGa                                                                                     <  2:534153/148‑1 (MQ=255)                                                                           cAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                        >  1:682338/1‑150 (MQ=255)                                                                            aggggaccgcGCGAACCGGAACGGTGGTGTATCTCGAACATGAAAC‑CCGTTATAAGTATCATAGGTCAAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                                       <  2:994202/144‑1 (MQ=255)                                                                             ggtccgcgcgcgTACCGGACCCGTGTTTTATCTCGTACCGTTAAC‑CCCCTATCGGGATAATATAACCAACCCCCTCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                     <  2:750917/145‑1 (MQ=255)                                                                                cgccgcGCGTCCCGGACCGGTGTTGTACCTCGAACCGTTAAA‑CCGCTATCAGAATCATATGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAata                                                                    <  1:948907/149‑1 (MQ=255)                                                                                cgccgcGCGTCCCGAACCCGTGGTGTACCTCGAACCGTAACC‑CCGCTATCAGAATCATATAACCACCCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                     <  1:668256/148‑1 (MQ=255)                                                                                 gccgcGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                 >  2:761296/1‑151 (MQ=255)                                                                                      gcgtgccagaccgggggttTACCTCGACCCGTAAAC‑CCACTACAAGGATAATAGGATCACCTCCCCCGCCAATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaagaa                                                            <  2:155015/136‑1 (MQ=255)                                                                                       cgTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                             >  1:271734/1‑149 (MQ=255)                                                                                           cggtaaCGGTGTTGTACCCCAACCCGTTAAC‑CCGTTATAAGGATAATATAATAACCCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                        <  2:821560/130‑1 (MQ=255)                                                                                           ccGGAACCGTGGTTTATCCCAACCCGTAAAC‑CCGCTATCAGGATCATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                         <  2:500376/149‑1 (MQ=255)                                                                                             ggaccggtggtgTATCCCGACCCGTTAAC‑CCCTTATCAGAATCAAAAAAAAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                      <  2:302988/144‑1 (MQ=255)                                                                                                   gtgttgTATCCCGAACCTTAAAA‑CCGTTATCAGGATCATATGATCACCACCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                       <  2:328868/143‑1 (MQ=255)                                                                                                   gtggtgTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                               >  1:998070/1‑151 (MQ=255)                                                                                                    tggtgTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                               >  1:156176/1‑150 (MQ=255)                                                                                                       tttaccccaaccttttAAC‑CCGTTTTCAGGATCATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                  <  2:397708/130‑1 (MQ=255)                                                                                                       tgtATCTCGACCCTTTAAC‑CCGCTATCAGTATCATATCACCACCCCCCTCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                     <  1:639383/141‑1 (MQ=255)                                                                                                              cGAACCGTTAGA‑CGGCTATCCCGATCATATGACCAGCACGCTCCCCGATACCCGCCGGTCCATCGTCGGAAACGATCTTCTGCATGCACAGATTATCGGCGCTTTCTATCAAAGAAATATCGAGGGAGATAACCTGGCGCAGGCGCTGCAt                                    >  2:547356/1‑151 (MQ=255)                                                                                                                    gTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAc                              >  2:839160/1‑151 (MQ=255)                                                                                                                      tAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                             >  2:821236/1‑150 (MQ=255)                                                                                                                        aacccGCTATCAGAATAATATGACCACCCCCCTGGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                             <  1:155723/146‑1 (MQ=255)                                                                                                                        aa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGCTCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                           >  2:752809/1‑150 (MQ=255)                                                                                                                            cccTAACAGGATAATATGAACAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                       <  1:117437/149‑1 (MQ=255)                                                                                                                              ctttcggtataatatGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCt                      <  2:39429/139‑1 (MQ=255)                                                                                                                                       tCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAt            >  1:236329/1‑151 (MQ=255)                                                                                                                                            taaccAACCCCCCCGCCGGTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt          <  1:119173/144‑1 (MQ=255)                                                                                                                                                 aaCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTg  >  2:568758/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                    TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376359‑1376652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑