Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,986,048	C→G	8.6%	P97R (CCG→CGG)	flgA →	flagella basal body P‑ring formation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,986,048	0	C	G	8.6%	168.6 / 4.1	56	P97R (CCG→CGG)	flgA	flagella basal body P‑ring formation protein
Reads supporting (aligned to +/- strand):  ref base C (24/27);  new base G (3/2);  total (27/29)
Fisher's exact test for biased strand distribution p-value = 6.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGACGTGGC  >  NC_002947/4985905‑4986195                                                                                                                                                |                                                                                                                                                     tCTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGATAGCCCGGCCCAGCCGCTg                                                                                                                                                  <  3:94021/148‑1 (MQ=255) tCTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTg                                                                                                                                                  <  6:101427/148‑1 (MQ=255)  cTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTggg                                                                                                                                                >  3:41408/1‑149 (MQ=255)  cTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTggg                                                                                                                                                >  1:295924/1‑149 (MQ=255)     gAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGc                                                                                                                                               <  4:38244/147‑1 (MQ=255)     gAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCg                                                                                                                                             >  2:18151/1‑149 (MQ=255)      aaTTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCg                                                                                                                                             <  2:295924/148‑1 (MQ=255)           aCCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCgtgt                                                                                                                                          <  1:184356/146‑1 (MQ=255)           aCCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCgtgt                                                                                                                                          >  2:184356/1‑146 (MQ=255)                tGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACACACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTAc                                                                                                                                  >  4:28271/1‑149 (MQ=255)                 gAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTAc                                                                                                                                  <  6:281939/148‑1 (MQ=255)                  aaGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACgg                                                                                                                                <  5:53192/149‑1 (MQ=255)                  aaGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACg                                                                                                                                 >  7:219246/1‑148 (MQ=255)                             tCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑g                                                                                                                       <  3:238378/146‑1 (MQ=255)                                accaccCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTgg                                                                                                                                                 >  7:114352/1‑118 (MQ=255)                                             ccggccgCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACg                                                                                                                           <  6:289785/127‑1 (MQ=255)                                             ccggccgCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACg                                                                                                                           >  5:289785/1‑127 (MQ=255)                                              cggccgCTATGAACTCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGa                                                                                                   <  6:88357/149‑1 (MQ=255)                                                gccgCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACg                                                                                                 <  2:218016/149‑1 (MQ=255)                                                       tGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCTCGCAACGGCGCAGCACCGTGGACGGTATTc                                                                                           <  1:200681/149‑1 (MQ=255)                                                       tGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTAtt                                                                                            <  8:219246/147‑1 (MQ=255)                                                            tCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCg                                                                                     <  1:18151/149‑1 (MQ=255)                                                                  tCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACTGTATTCGTGCCGGCCAcc                                                                               <  4:41408/149‑1 (MQ=255)                                                                  tCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCAcc                                                                               >  5:277665/1‑149 (MQ=255)                                                                       ccGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGc                                                                           >  1:21170/1‑148 (MQ=255)                                                                                  aCGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTcc                                                                  >  6:109691/1‑146 (MQ=255)                                                                                  aCGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTcc                                                                  <  5:109691/146‑1 (MQ=255)                                                                                   cGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGa                                                              <  2:21170/149‑1 (MQ=255)                                                                                    gCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGAc                                                             >  1:300318/1‑149 (MQ=255)                                                                                                cGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACgtggtggtggtg                                                 <  2:300318/149‑1 (MQ=255)                                                                                                       cagccagcAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACgtggtgg                                                      <  3:35551/137‑1 (MQ=255)                                                                                                       cagccagcAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACgtggtgg                                                      >  4:35551/1‑137 (MQ=255)                                                                                                       cagccagcAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTCGGCCGTGTCACGCTACGGATACGCT‑GCAACGGCGCAGCACCCTGGACGGTATTCGTGCCGGCCACCGACCGACTAATCCGCGACGTGGTGGTGGTGAcccgcc                                          >  6:85759/1‑149 (MQ=255)                                                                                                           cggcagcTGGACGCCTCACTCGACACCCCGGCCCAGCGGCGGGGCCGCGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCt                                      <  5:110913/147‑1 (MQ=255)                                                                                                                     aCGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGac                            <  6:277665/149‑1 (MQ=255)                                                                                                                      cGCCTCACTGGAAAGCCCGGCCCAGCCGCTCGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGac                            >  3:36974/1‑148 (MQ=255)                                                                                                                           cACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACg                      >  5:71289/1‑149 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTc                   >  3:78470/1‑147 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTc                   <  4:78470/147‑1 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCgg                 >  4:225017/1‑149 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCgg                 >  6:129515/1‑149 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGAATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAgcgc                               <  4:290688/135‑1 (MQ=255)                                                                                                                                gAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGAATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAgcgc                               >  3:290688/1‑135 (MQ=255)                                                                                                                                 aaaGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGc                >  8:199146/1‑149 (MQ=255)                                                                                                                                 aaaGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGc                >  5:291884/1‑149 (MQ=255)                                                                                                                                    gCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGaa             <  4:36974/149‑1 (MQ=255)                                                                                                                                     cccGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACgtggtgg                                                      >  5:178444/1‑107 (MQ=255)                                                                                                                                     cccGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACgtggtgg                                                      <  6:178444/107‑1 (MQ=255)                                                                                                                                      acGGCCCAGCGGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAgg           >  8:13888/2‑149 (MQ=255)                                                                                                                                      acGGCCCAGCGGCTGGGCCGTGTGAAGGTACGGATACGCT‑GCAACGGCGCAGAAACGTGGACGGTATTCGTGCCGGCCACCTTGCGACTTTACCGCGACGTGGTGCTGGTGACCCGCCCGCTCAAGAGCGACACCACGGTAGGCGAAgg           >  2:255262/2‑149 (MQ=255)                                                                                                                                         gCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGa        <  3:225017/149‑1 (MQ=255)                                                                                                                                          cccAGCGGCTGGGCTGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGAc       >  2:104128/1‑149 (MQ=255)                                                                                                                                          cccAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAg            <  7:137195/144‑1 (MQ=255)                                                                                                                                          cccAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAg            >  8:137195/1‑144 (MQ=255)                                                                                                                                            cAGCGGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGACGt     <  7:13888/149‑1 (MQ=255)                                                                                                                                             aGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGACGTg    <  5:85759/149‑1 (MQ=255)                                                                                                                                               ccGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGACGTGGc  >  7:83038/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                     TCTTGAATTCACCGTTGAAGATTATCTGTCCACCACCCAGACTGCCGGCCGCTATGAAATCCAGGTCAACCCGCTGGACCCACGCCTGCGCATGCCGTTGTGCAGCCAGCAGCTGGACGCCTCACTGGAAAGCCCGGCCCAGCCGCTGGGCCGTGTGACGGTACGGATACGCT‑GCAACGGCGCAGCACCGTGGACGGTATTCGTGCCGGCCACCGTGCGACTTTTCCGCGACGTGGTGGTGGTGACCCGCCCGCTCAAGCGCGACAACACGGTCGGCGAAGGTGACGTGGC  >  NC_002947/4985905‑4986195

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑