Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,969,527	Δ1 bp	8.7%	coding (716/2064 nt)	fliC ←	flagellin

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,969,527	0	G	.	8.7%	139.2 / 7.3	46	coding (716/2064 nt)	fliC	flagellin
Reads supporting (aligned to +/- strand):  ref base G (23/18);  new base . (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.27e-01

TGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCT  >  NC_002947/4969381‑4969667                                                                                                                                                   |                                                                                                                                             tGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtg                                                                                                                                            >  5:409018/1‑149 (MQ=255)   gCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggt                                                                                                                                          <  6:381943/149‑1 (MQ=255)    cATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtg                                                                                                                                         <  3:315790/149‑1 (MQ=255)        gATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     <  5:240890/149‑1 (MQ=255)         aTGGTGAATGCCTGGATGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggt                                                                                                                                    <  2:76243/149‑1 (MQ=255)          tGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtg                                                                                                                                   <  6:409018/149‑1 (MQ=255)              gAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     <  6:424091/143‑1 (MQ=255)              gAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtgg                                                                                                                                     >  5:424091/1‑143 (MQ=255)               aaTGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTAc                                                                                                                               <  8:61570/148‑1 (MQ=255)                    cTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTCTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGt                                                                                                                         >  4:323048/1‑149 (MQ=255)                        gTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAg                                                                                                                     >  3:278902/1‑149 (MQ=255)                              tCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCaa                                                                                                               <  2:303044/149‑1 (MQ=255)                              tCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTACAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTAACCAAGTTCAGCACGaa                                                                                                               >  5:392021/1‑149 (MQ=255)                                      cAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTAcc                                                                                                         <  4:106336/147‑1 (MQ=255)                                         tGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcag                                                                                                    >  3:98403/1‑149 (MQ=255)                                            aCCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTACAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 >  1:15925/1‑149 (MQ=255)                                              cAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCGGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcagca                                                                                               >  8:77466/1‑149 (MQ=255)                                              cAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTCTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcagca                                                                                               >  1:266673/1‑149 (MQ=255)                                                gTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCAcc                                                                                             >  7:86446/1‑149 (MQ=255)                                                 tGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 <  7:212263/144‑1 (MQ=255)                                                 tGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGgcagcag                                                                                                 >  8:212263/1‑144 (MQ=255)                                                   gcgcTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGAt                                                                                          <  8:86446/149‑1 (MQ=255)                                                      cTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAACTTACAGCCAGCAGCACCGATGGt                                                                                       >  7:192196/1‑149 (MQ=255)                                                             tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    >  4:231409/1‑142 (MQ=255)                                                             tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    <  3:231409/142‑1 (MQ=255)                                                             tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    <  5:47670/142‑1 (MQ=255)                                                             tGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGA‑‑‑TGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCgg                                                                                    >  6:47670/1‑142 (MQ=255)                                                               cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTAt                                                                               >  6:302963/1‑148 (MQ=255)                                                               cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  4:278902/149‑1 (MQ=255)                                                               cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  4:98403/149‑1 (MQ=255)                                                               cTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTACAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTAt                                                                               <  2:15925/148‑1 (MQ=255)                                                                tAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              >  5:415978/1‑148 (MQ=255)                                                                  gctgTAACACCTGTATTTATAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCTATGTTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCaaa                                                                           <  6:392021/146‑1 (MQ=255)                                                                  gCGGTAACACCTGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATc                                                                              <  3:323048/146‑1 (MQ=255)                                                                                 ttGCTAGTCTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTg                                                             <  2:266673/148‑1 (MQ=255)                                                                                         ttCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCca                                                    >  1:373438/1‑149 (MQ=255)                                                                                          atgtggTTGACAATATCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCca                                                    >  7:325964/5‑148 (MQ=255)                                                                                              ggTTGATATTGTCCACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAAcc                                               <  5:302963/149‑1 (MQ=255)                                                                                              ggTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtgg                                                                                                                                  <  3:192897/66‑1 (MQ=255)                                                                                              ggTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGAtggtggtggtggtgg                                                                                                                                  >  4:192897/1‑66 (MQ=255)                                                                                               gTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAAcc                                               >  3:70576/1‑148 (MQ=255)                                                                                                       tGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACaa                                                 >  2:275576/1‑138 (MQ=255)                                                                                                       tGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACaa                                                 <  1:275576/138‑1 (MQ=255)                                                                                                            aCCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgct                                 >  3:364883/1‑149 (MQ=255)                                                                                                              cacaTCCTGCAGGGTGTCGCCTGCCGCGGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGtgctgc                               <  7:77466/149‑1 (MQ=255)                                                                                                                              tCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGcc               >  4:35377/1‑149 (MQ=255)                                                                                                                                gCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCa                             >  3:183467/1‑133 (MQ=255)                                                                                                                                gCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCa                             <  4:183467/133‑1 (MQ=255)                                                                                                                                   tGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAttgt                      >  2:267480/1‑137 (MQ=255)                                                                                                                                   tGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAttgt                      <  1:267480/137‑1 (MQ=255)                                                                                                                                      cGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAtt                        <  6:417532/132‑1 (MQ=255)                                                                                                                                      cGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCAtt                        >  5:417532/1‑132 (MQ=255)                                                                                                                                        cagcagCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCg     >  3:186872/1‑149 (MQ=255)                                                                                                                                           cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACt          <  2:233357/141‑1 (MQ=255)                                                                                                                                           cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACt          >  1:233357/1‑141 (MQ=255)                                                                                                                                           cagcGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCt  <  4:70576/149‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                             TGGCATCGATGGTGAATGCCTGGGTGCCGTCGAGCTTCAGTGCACCAGTGGCGCTGTCAATGCTAGCGGTAACACCGGTATTGCTAGTTTCCAGGTTGATATTGTCAACCACATCCTGCAGGGTGTCGCCTGCCGCAGCAGCGATGGTGGTGGTGGTGGTACCAACGTTCAGCACCAAGTTACCGGCAGCAGCACCGATGGTCGGCTTATCAAATACGCCCGCGCCTGCAGTACCCACAACCGAAGCAGAAGTGCTGCCAGCATTGTTGGTGCCGAACTTACCGGCT  >  NC_002947/4969381‑4969667

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: ‑