Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,536,386	G→A	7.7%	L8L (CTG→CTA)	PP_3125 →	Cro/CI family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,536,386	0	G	A	7.7%	151.6 / 3.2	54	L8L (CTG→CTA)	PP_3125	Cro/CI family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (20/29);  new base A (2/2);  total (23/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.79e-01

TGGGCGCTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGGCGCTGAACGTCAAT  >  NC_002947/3536239‑3536527                                                                                                                                                    |                                                                                                                                               tgGGCGCTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACtgctgc                                                                                                                                               <  8:75437/149‑1 (MQ=255) tgGGCGCTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACtgctgc                                                                                                                                               <  5:172671/149‑1 (MQ=255) tgGGCGCTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACtgctgc                                                                                                                                               <  6:72300/149‑1 (MQ=255)     cgcTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTaa                                                                                                                                           <  6:153990/149‑1 (MQ=255)       cTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGa                                                                                                                                         <  6:34051/149‑1 (MQ=255)            tACAACGATGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTTGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tg                                                                                                                                   >  8:296654/1‑149 (MQ=255)              cAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tggg                                                                                                                                 <  4:108514/149‑1 (MQ=255)              cAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tgg                                                                                                                                  <  5:134161/148‑1 (MQ=255)              cAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tgg                                                                                                                                  <  4:55929/148‑1 (MQ=255)               aaCGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGATGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tgggg                                                                                                                                <  2:284131/149‑1 (MQ=255)               aaCGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGaaa                                                                                                                                       <  6:257991/143‑1 (MQ=255)               aaCGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGaaa                                                                                                                                       >  5:257991/1‑143 (MQ=255)               aaCGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑Tgggg                                                                                                                                <  8:283180/149‑1 (MQ=255)                tcGCTGCTGTCCGTGCCGCCAGTGTTGCCTTGATTCAAGGGCCCTGGAGGCTTGGCGTGAGCTTTCAGACGCGTATCATGGCTTCCTCAGCCTGGGACACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGa                                                                                                                               <  4:186534/148‑1 (MQ=255)                       aGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCt                                                                                                                        >  3:80888/1‑149 (MQ=255)                           cGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGaa                                                                                                                    <  4:148636/149‑1 (MQ=255)                                 gccAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTg                                                                                                              <  8:7704/149‑1 (MQ=255)                                  ccAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTgg                                                                                                             >  7:105362/1‑149 (MQ=255)                                   cAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGc                                                                                                            <  7:296654/149‑1 (MQ=255)                                             ttGATTCAAGGCCCCTGGAGGATTGGCGTCATCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGCAAACAGCCAGCACAAGAATAGCGCATT‑AAACTTCATCGGAAAAAACATGGGGATCACCGTGCAAATCGTGGCCGaaaacaat                                                                                                  >  6:144917/1‑145 (MQ=255)                                               gATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACt                                                                                                  <  1:312835/147‑1 (MQ=255)                                                 ttCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCTTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGc                                                                                               <  3:13929/148‑1 (MQ=255)                                                 ttCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGAGTATCATGGCTGCCTCAGCCTTGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGc                                                                                               <  1:314796/148‑1 (MQ=255)                                                    aaGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGa                                                                                           >  7:121761/1‑149 (MQ=255)                                                    aaGGCCCCTGGAGGCTTGGCGTCAGCGTTCAGACGCGTATCATCCCTGCCTCAGCCTGGGAAACTCGCGTCAAGTGACTATCCGATTGAAACTGCTGCCTAAGAAAC‑TCGGCATGCCACAGGAAATGATGGCCGAAAAGACTGGCATGa                                                                                           >  3:184000/1‑149 (MQ=255)                                                     aGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGAc                                                                                          <  1:10833/149‑1 (MQ=255)                                                           cTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAAt                                                                                                                  >  5:293003/1‑119 (MQ=255)                                                           cTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAAt                                                                                                                  <  6:293003/119‑1 (MQ=255)                                                                              tttCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCaaaa                                                                                     <  7:237699/129‑1 (MQ=255)                                                                              tttCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCaaaa                                                                                     >  8:237699/1‑129 (MQ=255)                                                                                tCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAgcg                                                               >  1:11418/1‑149 (MQ=255)                                                                                   gACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCgg                                                            >  3:99616/1‑149 (MQ=255)                                                                                          aTCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCaa                                                      <  8:105362/148‑1 (MQ=255)                                                                                             aTGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTACGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACg                                                  >  6:34878/1‑149 (MQ=255)                                                                                             aTGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTACGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACg                                                  >  6:30187/1‑149 (MQ=255)                                                                                                gCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCt                                                                                  <  3:48423/114‑1 (MQ=255)                                                                                                gCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCt                                                                                  >  4:48423/1‑114 (MQ=255)                                                                                                 cTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCt                                              <  4:99616/149‑1 (MQ=255)                                                                                                     cTCAGCCTGGGAAACTGGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAATC‑TGGGGATGACCATGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGAt                                          <  7:87254/149‑1 (MQ=255)                                                                                                          ccTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCaaa                                                                                      <  3:194073/100‑1 (MQ=255)                                                                                                          ccTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCaaa                                                                                      >  4:194073/1‑100 (MQ=255)                                                                                                            tGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGCCCAACCGCTACCTGGCCAAGGTCGAGCGCGGCCTCACCACGCCGTCGATCgcggcg                                   >  4:266009/1‑149 (MQ=255)                                                                                                              ggAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTgcggc                                 >  8:105459/1‑149 (MQ=255)                                                                                                                  aCTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGc                                                                                               <  3:213627/83‑1 (MQ=255)                                                                                                                  aCTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGc                                                                                               >  4:213627/1‑83 (MQ=255)                                                                                                                    tCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTAc                                                                                >  6:118418/1‑96 (MQ=255)                                                                                                                    tCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTAc                                                                                <  5:118418/96‑1 (MQ=255)                                                                                                                           acaTGTCTATCCGATTGAAACTGCTACGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGc                     <  5:30187/148‑1 (MQ=255)                                                                                                                           acaTGTCTATCCGATTGAAACTGCTACGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGc                     <  5:34878/148‑1 (MQ=255)                                                                                                                            caTGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGa                   <  4:80888/149‑1 (MQ=255)                                                                                                                                tCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAggg                <  7:105459/148‑1 (MQ=255)                                                                                                                                  tATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGgcgc             >  7:110285/1‑149 (MQ=255)                                                                                                                                       gATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGGCGCTGCAc        >  4:71060/1‑149 (MQ=255)                                                                                                                                        aTTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGGCGCTGAACg       >  3:241662/1‑149 (MQ=255)                                                                                                                                             aaCTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGGCGCTGAACGTCAAt  <  3:266009/149‑1 (MQ=255)                                                                                                                                              aCTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCaa                                                      >  3:257199/1‑96 (MQ=255)                                                                                                                                              aCTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCaa                                                      <  4:257199/96‑1 (MQ=255)                                                                                                                                                    |                                                                                                                                               TGGGCGCTGGGTACAACGCTGCAGTACGTGCCGCCAGTGATGCCTTGATTCAAGGCCCCTGGAGGCTTGGCGTCAGCTTTCAGACGCGTATCATGGCTGCCTCAGCCTGGGAAACTCGCGTCACATGTCTATCCGATTGAAACTGCTGCGTAAGAAAC‑TGGGGATGACCCTGGAAATGCTGGCCGAAAAGACTGGCATGACCAAAAGCTACCTGTCCAAGGTCGAGCGCGGCCTCAACACGCCCTCGATCGCTGCGGCGCTGAAACTGGCGAGGGCGCTGAACGTCAAT  >  NC_002947/3536239‑3536527

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: ‑