Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,751,071:1	+C	8.7%	coding (430/855 nt)	PP_1551 →	replication protein O

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,751,071	1	.	C	8.7%	171.8 / 9.9	46	coding (430/855 nt)	PP_1551	replication protein O
Reads supporting (aligned to +/- strand):  ref base . (16/26);  new base C (2/2);  total (18/28)
Fisher's exact test for biased strand distribution p-value = 6.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

AATGACCCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGC  >  NC_002947/1750927‑1751219                                                                                                                                                  |                                                                                                                                                     aaTGACCCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTTTGTAA‑ATct                                                                                                                                                  <  8:258035/149‑1 (MQ=255)  aTGACCCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATctt                                                                                                                                                 >  6:129003/1‑149 (MQ=255)       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                                                                                                                                            >  4:347793/1‑133 (MQ=255)                       aCGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttccttc                                                                                                                                            <  3:347793/133‑1 (MQ=255)                         gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtaggg                                                                                                                          <  1:277861/149‑5 (MQ=255)                         gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtagg                                                                                                                           >  3:379121/1‑145 (MQ=255)                         gTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAACATCTTCCGAAGGAAGAT‑TTACAtagg                                                                                                                           <  4:379121/148‑4 (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)                                                  ccGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttcc                                                                                                                                               <  6:362844/103‑1 (MQ=255)                                                  ccGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATcttcc                                                                                                                                               >  5:362844/1‑103 (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   <  8:207667/148‑1 (MQ=255)                                                                                                                                                 a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg   <  5:264204/148‑1 (MQ=255)                                                                                                                                                 a‑aTCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTgg   <  3:52922/148‑1 (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)                                                                                                                                                  |                                                                                                                                                     AATGACCCGAAGGACTGGATTTACGTTGATCCGAAACAGACCAAAACAGCCGACTCGGCTGAAGTGGTCCGAATCGGCTCAGAGTCGAAACAGACCAAAACCGCCGACTCCCTTCTTTATTCTAAGAAAGAAACCCCCTATGTAA‑ATCTTCCTTCGGAAGATGTTACATGCCCCCCCAGCGAGCCGGAGCCGACTCCGGCCAAGGATGAGCGCAAGGCTCCCTTCGGCAAAGCCGCCATGCTGGCCGACAATCCGCACGGGCTCGATGAATCCCTGATCGCTGATTACTTGGC  >  NC_002947/1750927‑1751219

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: ‑