Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,959,920	T→C	7.8%	D184G (GAT→GGT)	fliF ←	flagellar M‑ring protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,959,920	0	T	C	7.8%	137.0 / 2.9	51	D184G (GAT→GGT)	fliF	flagellar M‑ring protein
Reads supporting (aligned to +/- strand):  ref base T (24/23);  new base C (2/2);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

CCTTCTGGTCGACGACGGTGACCTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCATGAACTGGCTGGTGCCCAGGCCCTG  >  NC_002947/4959774‑4960068                                                                                                                                                    |                                                                                                                                                     ccTTCTGGTCGACGACGGTGACCTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑tcat                                                                                                                                                      <  7:111152/147‑1 (MQ=255) ccTTCTGGTCGACGACGGTGACCTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑tcat                                                                                                                                                      >  8:111152/1‑147 (MQ=255)                cgGTGACCTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGaa                                                                                                                                     >  7:206894/1‑149 (MQ=255)                       cTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCg                                                                                                                              >  2:209993/1‑149 (MQ=255)                          ggATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGa                                                                                                                           <  1:186446/149‑1 (MQ=255)                            aTTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGaa                                                                                                                                     <  3:17098/137‑1 (MQ=255)                            aTTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGaa                                                                                                                                     >  4:17098/1‑137 (MQ=255)                             tttGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATgg                                                                                                                        >  8:61278/1‑149 (MQ=255)                             tttGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATgg                                                                                                                        <  7:61278/149‑1 (MQ=255)                                 tCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAg                                                                                                                    >  7:40497/1‑149 (MQ=255)                                 tCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAg                                                                                                                    >  8:79214/1‑149 (MQ=255)                                  ccAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGATGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAgg                                                                                                                   >  6:21948/1‑149 (MQ=255)                                   cAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGt                                                                                                                  >  4:324853/1‑149 (MQ=255)                                      ttCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCa                                                                                                               <  8:206894/149‑1 (MQ=255)                                                 tggtggCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCg                                                                                                                              <  4:212870/123‑1 (MQ=255)                                                 tggtggCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCg                                                                                                                              >  3:212870/1‑123 (MQ=255)                                                 tggtggCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCAc                                                                                                              <  7:25006/139‑1 (MQ=255)                                                 tggtggCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCAc                                                                                                              >  8:25006/1‑139 (MQ=255)                                                   gtggCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCt                                                                                                   <  7:21220/148‑1 (MQ=255)                                                      gCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGa                                                                                                <  1:90396/148‑1 (MQ=255)                                                              gTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGa                                                                                                <  3:146712/140‑1 (MQ=255)                                                              gTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGa                                                                                                >  4:146712/1‑140 (MQ=255)                                                              gTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACgttgtt                                                                                         >  2:339597/1‑147 (MQ=255)                                                              gTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGCATGGCCAGGTGCACGCGCGCGGCCTTGACgttgtt                                                                                         >  1:147855/1‑147 (MQ=255)                                                                   cGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTg                                                                                  <  1:339597/149‑1 (MQ=255)                                                                         ccATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACGAGTACCGATGCTCTGGGCTTGCGT‑TCATCTCGCACTAACAGCGAACTTTTCGGGATGGCCAGGTGCTCGCGCGCGGCCTTGACGTTGTTGAGGCTgg                                                                                 <  1:7667/144‑1 (MQ=255)                                                                         ccATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGAGCACGAGCGCGGCCTTGACGTTGTTGAGGCTGGaagat                                                                            >  2:7667/1‑146 (MQ=255)                                                                          cATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACgg                                                                           <  2:147855/149‑1 (MQ=255)                                                                            tCACCTGCCCGGCTTCCAGTGCACGGGCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCACCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACgttg                                                                                           >  1:10579/1‑131 (MQ=255)                                                                            tCACCTGCCCGGCTTCCAGTGCACGGGCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCACCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACgttg                                                                                           >  1:4854/1‑131 (MQ=255)                                                                            tCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCACCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACgttg                                                                                           <  2:4854/131‑1 (MQ=255)                                                                            tCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCACCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACgttg                                                                                           <  2:10579/131‑1 (MQ=255)                                                                               ccTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGt                                                                      <  8:40497/149‑1 (MQ=255)                                                                               ccTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGACACGTGCACGCGCGCGGCCTTGACGGTGTTGAGGCTTGAAACGGTACGt                                                                      >  4:234968/1‑149 (MQ=255)                                                                                   cccGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGc                                                                    <  7:79214/147‑1 (MQ=255)                                                                                    ccGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGACACGGTACGTGCCAg                                                                 >  4:87767/1‑149 (MQ=255)                                                                                         ttCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCCGGTGCACGCGCGCGGCCTTGAc                                                                                               <  7:222080/114‑1 (MQ=255)                                                                                         ttCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGAc                                                                                               >  8:222080/1‑114 (MQ=255)                                                                                              gTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTcc                                                       <  5:21948/149‑1 (MQ=255)                                                                                                  aCGTCCTGGGTACAGCTCGACCAGTACGGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGc                                                   <  1:209993/149‑1 (MQ=255)                                                                                                  aCGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGc                                                   >  2:229491/1‑149 (MQ=255)                                                                                                             aCAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAg                                        >  3:159100/1‑149 (MQ=255)                                                                                                                  tCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGt                                   >  7:204008/1‑149 (MQ=255)                                                                                                                   cGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTg                                  <  1:229491/149‑1 (MQ=255)                                                                                                                    gACCAGTACCGAGGCGCTGGGCTTGCGTGTCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGt                                   >  1:197259/1‑148 (MQ=255)                                                                                                                    gACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGt                                   <  2:197259/147‑1 (MQ=255)                                                                                                                    gACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGATGCGGCGGTAGCGGGTgg                                 >  7:244893/1‑149 (MQ=255)                                                                                                                        aGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTc                             <  8:204008/149‑1 (MQ=255)                                                                                                                         gTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTcc                            <  3:87767/149‑1 (MQ=255)                                                                                                                            ccGAGGCGCGGGGCGTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCAt                          <  3:234968/148‑1 (MQ=255)                                                                                                                               aGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGc                                                                    <  2:10163/103‑1 (MQ=255)                                                                                                                               aGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGc                                                                    >  1:10163/1‑103 (MQ=255)                                                                                                                                              gT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCATGAACTGGCTGGTGCCCAgg       >  2:270727/1‑149 (MQ=255)                                                                                                                                                   atcaCGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCATGAACTGGCTGGTGCCCAGGCCCt   >  4:218991/1‑149 (MQ=255)                                                                                                                                                    tcaCGCACGAACACTGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCATGAACTGGCTGGTGCCCAGGCCCTg  >  2:177195/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     CCTTCTGGTCGACGACGGTGACCTGGGATTTGTCCAGTTCCGGCACGCTGGTGGCGACCAGGTTGACGATGGCCATCACCTGCCCGGCTTCCAGTGCACGGCCTGGGTACAGCTCGACCAGTACCGAGGCGCTGGGCTTGCGT‑TCATCACGCACGAACACCGAACTTTTCGGGATGGCCAGGTGCACGCGCGCGGCCTTGACGTTGTTGAGGCTGGAAACGGTACGTGCCAGTTCGCCTTCCAGGCTGCGGCGGTAGCGGGTGGCTTCCATGAACTGGCTGGTGCCCAGGCCCTG  >  NC_002947/4959774‑4960068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑