Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,316,914	G→C	11.5%	intergenic (‑117/+56)	ribC ← / ← treSA	riboflavin synthase/trehalose synthase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,316,914	0	G	C	11.5%	143.8 / 11.0	52	intergenic (‑117/+56)	ribC/treSA	riboflavin synthase/trehalose synthase A
Reads supporting (aligned to +/- strand):  ref base G (23/23);  new base C (2/4);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 6.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GGGCGGACGGCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTCGGTCAAATCGC  >  NC_002947/3316766‑3317061                                                                                                                                                     |                                                                                                                                                      gggCGGACGGCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCggg                                                                                                                                                       <  5:324902/149‑1 (MQ=255)     ggACGGCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAg                                                                                                                                                   >  8:31966/1‑149 (MQ=255)         ggCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAcgcgg                                                                                                                                               >  8:151791/1‑149 (MQ=255)         ggCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCCCCGCGCAggcgc                                                                                                                                               <  6:353171/149‑2 (MQ=255)          gCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAggcggc                                                                                                                                              >  8:236073/1‑149 (MQ=255)          gCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCCCCGCGCAggcgcc                                                                                                                                              <  4:124869/149‑3 (MQ=255)           ccTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGgcggcg                                                                                                                                             >  7:17906/1‑149 (MQ=255)              ggACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGc                                                                                                                                          >  3:6960/1‑149 (MQ=255)              ggACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGc                                                                                                                                          >  1:146849/1‑149 (MQ=255)               gACGATGGCGGTGTACATGGAGTTGCTCCTCGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGGCTGGCGCCTGCGCGGGGCAGGCGGCGTGc                                                                                                                                          <  4:51611/148‑1 (MQ=255)                    tGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTgg                                                                                                                                    <  7:31966/149‑1 (MQ=255)                    tGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTgg                                                                                                                                    <  5:63632/149‑1 (MQ=255)                              cATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCgg                                                                                                                          <  4:224149/149‑1 (MQ=255)                              cATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCg                                                                                                                           <  4:235974/148‑1 (MQ=255)                               aTGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGt                                                                                                                         >  2:1849/1‑149 (MQ=255)                               aTGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGt                                                                                                                         <  1:379916/149‑1 (MQ=255)                               aTGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGt                                                                                                                         <  1:1849/149‑1 (MQ=255)                                       gCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGAc                                                                                                                <  4:55582/148‑1 (MQ=255)                                        cTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACg                                                                                                               <  7:156660/148‑1 (MQ=255)                                         cacTGGGCACGCAAAAAAAAAATTCCCAACGCTATCCCCGTTCCGCATTAAATTCAATACCAGGCTTCCTGGTTGGCAATCCGGTTTGCTTTTTTGGCGCCTGCGCGGGGCTGGGGGGGTGCTTTTAGGCGAAACCGGTT‑‑TGCGACGGc                                                                                                             <  7:236073/147‑1 (MQ=255)                                              ggCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑GGCGACGGCATGGc                                                                                                        >  2:334396/1‑149 (MQ=255)                                                   ggAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGc                                                                                                   <  7:151791/149‑1 (MQ=255)                                                                 ccGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACAt                                                                                      <  6:191726/148‑1 (MQ=255)                                                                         tATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCgctgc                                                                             >  5:282713/1‑149 (MQ=255)                                                                         tATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCgctgc                                                                             >  3:186434/1‑149 (MQ=255)                                                                             cccGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGtt                                                                         <  3:246866/149‑1 (MQ=255)                                                                              ccGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTg                                                                        <  3:315157/149‑1 (MQ=255)                                                                                 tAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGAc                                                                      >  6:129156/1‑148 (MQ=255)                                                                                    cgcAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATc                                                                  <  1:167788/149‑1 (MQ=255)                                                                                     gcAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATcc                                                                 >  7:28007/1‑149 (MQ=255)                                                                                      cAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATTCCCGCTGCTCTTGACGATCCg                                                                >  6:213522/1‑149 (MQ=255)                                                                                       aGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCCGATTCAAACATGCCCGCTGCTGTTGACGATCCg                                                                >  6:184001/1‑148 (MQ=255)                                                                                       aGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCg                                                                >  4:71537/1‑148 (MQ=255)                                                                                              gCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATgg                                                                                                         <  4:213839/100‑1 (MQ=255)                                                                                              gCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATgg                                                                                                         >  3:213839/1‑100 (MQ=255)                                                                                                aaGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAgc                                                      >  1:191368/1‑149 (MQ=255)                                                                                                        gCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTa                                              <  6:131857/149‑1 (MQ=255)                                                                                                        gCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGCGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGt                                                                          <  4:32514/121‑1 (MQ=255)                                                                                                        gCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGCGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGt                                                                          >  3:32514/1‑121 (MQ=255)                                                                                                              tggctggcAAGCCGGCTTGCGAGTCTCGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTTAAGGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACggg                                          >  1:117929/1‑149 (MQ=255)                                                                                                                gctggcAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTcc                                       <  8:17906/148‑1 (MQ=255)                                                                                                                      atgCCGGGTTGCGTGTCTTGCGCCTGGGCGGGGGAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGTCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCa                                <  2:146849/147‑1 (MQ=255)                                                                                                                           ggCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATc                           <  6:282713/149‑1 (MQ=255)                                                                                                                            gCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCa                          <  5:213522/149‑1 (MQ=255)                                                                                                                                gCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCAt                                                                                                           >  8:77726/1‑64 (MQ=255)                                                                                                                                gCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCAt                                                                                                           <  7:77726/64‑1 (MQ=255)                                                                                                                                 cGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTGCACCATCAGgcgc                     <  5:323894/149‑1 (MQ=255)                                                                                                                                  gAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGcc                    >  4:144015/1‑149 (MQ=255)                                                                                                                                  gAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGcc                    >  5:102565/1‑149 (MQ=255)                                                                                                                                        gccgcCTGCCCCGCGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCt              >  3:212712/3‑149 (MQ=255)                                                                                                                                         gcgcCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTc             >  3:290212/1‑149 (MQ=255)                                                                                                                                          cgcCTGCCCCGCGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTCg            <  4:212712/149‑1 (MQ=255)                                                                                                                                           gcCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTCgg           >  7:207112/1‑149 (MQ=255)                                                                                                                                                    gggCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTCGGTCAAATCGc  <  4:6960/149‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                      GGGCGGACGGCCTGGACGATGCCGGTGTACATGGAGTTGCTCCTGGGCACGGAAAAGAAAACTTCCGAACGCTATGCCCGTAGCGCAGTAAATGCAAGACCAGGCTTCCTGGCTGGCAAGCCGGCTTGCGAGTCTGGCGCCTGCGCGGGGCAGGCGGCGTGCTTGTGGGCGAAACCGGTT‑‑TGCGACGGCATGGCCACGCCAGATTCAAACATGCCCGCTGCTGTTGACGATCCGCAGGCACAGCGCCTCGTACGGGTCCAGGTTCACCATCAGGCGCCCGTCCTCGGTCAAATCGC  >  NC_002947/3316766‑3317061

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: ‑