Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,368,609	Δ1 bp	7.7%	coding (1915/3015 nt)	PP_2964 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,368,609	0	A	.	7.7%	155.3 / 7.6	52	coding (1915/3015 nt)	PP_2964	transposase
Reads supporting (aligned to +/- strand):  ref base A (23/25);  new base . (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.30e-01

AGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAGGCGGTGGCTGCGGA  >  NC_002947/3368463‑3368754                                                                                                                                                    |                                                                                                                                                  ttcATTGGATTCTGTTCACGCGGCATTTCGGGGCCATGTCCGGTAACGTGCCGAAGCTCAAAGAGCCTGGCGAGCGCTAACTGATGACGTTCTTCGCCATGCGGCTGCAACCTAGGCGCTAGCCAGGCTGCACGGCATCTGACCGGTaa                                                                                                                                                  <  1:252796/147‑1 (MQ=255)    aTTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGt                                                                                                                                               >  1:82118/1‑148 (MQ=255)        gATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACg                                                                                                                                           <  7:17034/148‑1 (MQ=255)        gATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACg                                                                                                                                           <  3:262197/148‑1 (MQ=255)        gATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACg                                                                                                                                           >  4:262197/1‑148 (MQ=255)        gATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACg                                                                                                                                           >  8:17034/1‑148 (MQ=255)             aGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCcaca                                                                                                                                      >  8:175699/1‑148 (MQ=255)              gTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCcacaca                                                                                                                                    <  2:82118/149‑1 (MQ=255)                     cgGCATTTCGGGCCCATGTCCGGTTACTAGCCGAATCTCAAATAGCATGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCTGTAATGTCACGCCACACATGCTGTc                                                                                                                             <  7:286771/149‑1 (MQ=255)                     cgGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTc                                                                                                                             <  7:175699/149‑1 (MQ=255)                      ggCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTcc                                                                                                                            <  8:172517/149‑1 (MQ=255)                          tttCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCtaaa                                                                                                                        <  5:122424/149‑3 (MQ=255)                                gCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTc                                                                                                                             <  7:196638/138‑1 (MQ=255)                                gCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTc                                                                                                                             >  8:196638/1‑138 (MQ=255)                                   cATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGcc                                                                                                               <  6:221126/149‑1 (MQ=255)                                   cATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGcc                                                                                                               <  2:46080/149‑1 (MQ=255)                                              aCGAGCCGATGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCg                                                                                                    <  7:80104/149‑1 (MQ=255)                                                gAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCt                                                                                                  >  7:147729/1‑149 (MQ=255)                                                     gAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAATCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGCCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGaa                                                                                              >  2:191976/1‑148 (MQ=255)                                                             aaGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGa                                                                                      >  1:246332/1‑148 (MQ=255)                                                               gagCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAATCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGCCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACaa                                                                                   <  1:191976/149‑1 (MQ=255)                                                                    tGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCt                                                                               >  4:179086/1‑148 (MQ=255)                                                                    tGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCt                                                                               >  2:340859/1‑148 (MQ=255)                                                                     gCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTgg                                                                                       >  6:294609/1‑139 (MQ=255)                                                                     gCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTgg                                                                                       <  5:294609/139‑1 (MQ=255)                                                                                ccTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGa                                                                       >  3:129865/1‑144 (MQ=255)                                                                                ccTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGa                                                                       <  4:129865/144‑1 (MQ=255)                                                                                   gatgaCGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGGCGTCCCCTCTCGCTGGAAAAACGGGACAAGGCTAACCGCGCGTtggtgg                                                               >  6:136684/1‑149 (MQ=255)                                                                                    atgaCGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCt                                                                                                                           >  4:244294/1‑88 (MQ=255)                                                                                     tgaCGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGaa                                                             <  8:147729/149‑1 (MQ=255)                                                                                       aCGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAAc                                                            <  2:246332/148‑1 (MQ=255)                                                                                               cGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTAc                                                       <  3:179086/145‑1 (MQ=255)                                                                                                     g‑ggCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTtg                                                                   >  5:8169/1‑127 (MQ=255)                                                                                                     g‑ggCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTtg                                                                   <  6:8169/127‑1 (MQ=255)                                                                                                             aaCCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGcc                                      >  7:130822/1‑149 (MQ=255)                                                                                                              aCCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCcac                                                                                                                                       <  2:221643/51‑1 (MQ=255)                                                                                                              aCCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCcac                                                                                                                                       >  1:221643/1‑51 (MQ=255)                                                                                                              aCCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACcgc                                                                         >  6:117999/1‑113 (MQ=255)                                                                                                              aCCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACcgc                                                                         <  5:117999/113‑1 (MQ=255)                                                                                                                     cccTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGctct                              >  5:215242/1‑149 (MQ=255)                                                                                                                            cAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGctct                              >  5:57259/1‑142 (MQ=255)                                                                                                                            cAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGctct                              <  6:57259/142‑1 (MQ=255)                                                                                                                            cAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGa                       <  6:215242/149‑1 (MQ=255)                                                                                                                            cAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGa                       >  7:235583/1‑149 (MQ=255)                                                                                                                             aGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGa                       >  8:39797/1‑148 (MQ=255)                                                                                                                             aGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGa                       <  7:39797/148‑1 (MQ=255)                                                                                                                                 tacACGGCATCTGACCGGT‑ATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGc                   >  2:205716/3‑147 (MQ=255)                                                                                                                                 tacACGGCATCTGACCGGT‑ATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGc                   >  2:200587/3‑147 (MQ=255)                                                                                                                                   cACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAg                <  8:130822/149‑1 (MQ=255)                                                                                                                                   cACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAg                >  8:205029/1‑149 (MQ=255)                                                                                                                                              aCCGGT‑ATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAGGCGGTGGCTGCg    <  1:205716/149‑1 (MQ=255)                                                                                                                                              aCCGGT‑ATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAGGCGGTGGCTGCg    <  1:200587/149‑1 (MQ=255)                                                                                                                                                 ggTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAGGCGGTGGCTGCGGa  <  1:340859/149‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                                  AGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATG‑GGCTGCAACCTAGGCCCTAGCCAGGCTGCACGGCATCTGACCGGTAATGTCACGCCACACATGCTGTCCTATACGAATCGCCGTCACCTCTCGCTGGAAAAACTGGACAAGGCTAACCGCGAGTTGGTGGAACTCTACCTTCAACTTGATCTGCCCAAGCTCTGGGGCGATGGCAAGGCGGTGGCTGCGGA  >  NC_002947/3368463‑3368754

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: ‑