Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,751,081	C→A	16.5%	S147* (TCG→TAG) ‡	PP_1551 →	replication protein O

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,751,081	0	C	A	16.5%	100.0 / 9.6	46	S147* (TCG→TAG) ‡	PP_1551	replication protein O
Reads supporting (aligned to +/- strand):  ref base C (10/26);  new base A (5/3);  total (17/29)
Fisher's exact test for biased strand distribution p-value = 9.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.67e-01

CCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGC  >  NC_002947/1750933‑1751226                                                                                                                                                      |                                                                                                                                                  ccGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttccttc                                                                                                                                                   <  8:376683/149‑1 (MQ=255)        aCTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGAt                                                                                                                                            >  8:21679/1‑149 (MQ=255)         cTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATg                                                                                                                                           <  7:21679/149‑1 (MQ=255)         cTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTAATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATg                                                                                                                                           <  1:292557/149‑1 (MQ=255)          tGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAACACCGCCGACTACCTTCTTTATTCTAAGAAAGAAAACCCCTATGTAA‑ATATAACATCGTAAGATGt                                                                                                                                          >  2:348762/1‑149 (MQ=255)          tGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGACCCGCCCTATGTAA‑CTAATACTTCGGAAGATGt                                                                                                                                          >  8:322714/1‑149 (MQ=255)          tGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAAAGCCGTATGTAA‑ATATTAATTAGGAAGATGt                                                                                                                                          >  2:96808/1‑149 (MQ=255)            gATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAttta                                                                                                                                         >  2:277861/1‑146 (MQ=255)            gATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGtt                                                                                                                                         <  5:84440/148‑1 (MQ=255)             aTTTACGTTGATCCGAAACAGACCAAACCAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGGCGAAACAGACCAAACCCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCGAAGGAAGAT‑TTACa                                                                                                                                      <  3:307632/149‑1 (MQ=255)             aTTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTa                                                                                                                                        <  1:274479/148‑1 (MQ=255)                tACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTTAAGTGGTCCGAATCGGCTGATAGGCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACAt                                                                                                                                     <  1:135045/148‑1 (MQ=255)                tACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACAt                                                                                                                                     <  5:172352/148‑1 (MQ=255)                 aCGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttccttc                                                                                                                                                   <  3:347793/133‑1 (MQ=255)                 aCGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttccttc                                                                                                                                                   >  4:347793/1‑133 (MQ=255)                   gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtaggg                                                                                                                                 <  1:277861/149‑5 (MQ=255)                   gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtagg                                                                                                                                  <  4:379121/148‑4 (MQ=255)                   gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtagg                                                                                                                                  >  3:379121/1‑145 (MQ=255)                    ttGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTGCTTAGGAAGATGTTACAttcacc                                                                                                                                >  2:93296/1‑144 (MQ=255)                              aCAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGACGCCGCCGGTGTAA‑ATCTTCGTGCGGAAGATGTTACATGcgcgcccgccgggc                                                                                                                      >  7:207667/1‑142 (MQ=255)                                         cAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACt                                                                                                           <  5:129003/149‑1 (MQ=255)                                                   ggCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAGCGCCCTGTGTTA‑AGCTTGGGTCGGGGGATGTTAGATGGCGCGCCAGCGAGACGGAGCCGACGCCGGGCAAg                                                                                                  >  6:171002/1‑148 (MQ=255)                                                   ggCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCaa                                                                                                   <  7:27165/147‑1 (MQ=255)                                                              tCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAg                                                                                      <  7:322714/149‑1 (MQ=255)                                                                           agagTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCAATGTAA‑ATCTTCCGTGGGAAGATGTTAGATGCACCACCCCCGAGCCCGGGCCCACGCCGGCGAACGAGGACCCCCAGGCACCCGTCGGc                                                                          >  2:266313/1‑148 (MQ=255)                                                                             agTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCaaa                                                                       <  5:281798/149‑1 (MQ=255)                                                                              ttCGAAACAGACCAAAACCGCCCACTCGCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCaaa                                                                       <  1:348762/147‑1 (MQ=255)                                                                                       gACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAGGCCCCCTATGTAA‑ATCTTCCGTGGGTAGATGTTAGAGGGACACCCAGCGCGCCGGCGCCGCCTCCGGCCCACGCGGAGCGCACGGCGCCCGGCGGCCACGCCCCCAGGc                                                             >  6:308952/1‑149 (MQ=255)                                                                                           aaaaCCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTTTGTAA‑ATCTTCCTTCGTAAGATTTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGc                                                         <  2:202576/149‑1 (MQ=255)                                                                                           aaaaCCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGc                                                         <  5:171002/149‑1 (MQ=255)                                                                                            aaaCCGCCGACTCCCTTCTTTATTCTAAGAAAGAAAGGCCCTATGTAA‑ATATTGCTTAGGAAGATGTTACATGAACCACCAGCCAGCCGGAGCCGCAGCCGGCCAACGATGACCACAAGGCTCCCTACGGCAAAGCCGCCagacaggc                                                         >  4:43596/1‑141 (MQ=255)                                                                                            aaaCCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGcc                                                        <  3:43596/149‑1 (MQ=255)                                                                                             acccgccgACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCg                                                       <  7:327881/147‑1 (MQ=255)                                                                                                         ccTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCaaa                                                                       <  3:407931/121‑1 (MQ=255)                                                                                                             cttTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACggg                                         <  5:308952/147‑1 (MQ=255)                                                                                                                     tAAGAAAGAAGCCCCCTATGTAA‑ATCTTACTTCGGAAGATGTTAAATGAACCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCCGCAAAGCCGCCATGCAGGCCGACAAACACCACCGGCTCGATGaa                                >  4:52922/1‑148 (MQ=255)                                                                                                                           agaaaCCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGa                         <  6:254694/149‑1 (MQ=255)                                                                                                                                cccccTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATc                                                 <  5:233272/120‑1 (MQ=255)                                                                                                                                  cccTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCt                           <  4:82865/140‑1 (MQ=255)                                                                                                                                  cccTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCt                           >  3:82865/1‑140 (MQ=255)                                                                                                                                   ccTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGAt                 >  2:386449/1‑149 (MQ=255)                                                                                                                                         tAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACtt            <  3:91373/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCCCGGCCTCGATGAATCCCTGATCGCTCATTACTTGGc         >  8:64466/1‑149 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  5:264204/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  3:52922/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  8:207667/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  1:386449/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg          <  1:266313/148‑1 (MQ=255)                                                                                                                                           a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGc         >  4:307063/1‑149 (MQ=255)                                                                                                                                               cttccttcGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGt      >  3:231670/1‑149 (MQ=255)                                                                                                                                                    ttcGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGc  >  7:141544/1‑148 (MQ=255)                                                                                                                                                    ttcGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGc  >  6:93499/1‑148 (MQ=255)                                                                                                                                                    ttcGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGATGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGc  >  1:181440/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                                  CCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGCTGTCCGC  >  NC_002947/1750933‑1751226

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑