Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,984,455	G→A	10.0%	intergenic (+51/+38)	PP_5242 → / ← ycaC‑II	GAF domain‑containing sensor histidine kinase/putative hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,984,455	0	G	A	10.0%	130.7 / 4.6	50	intergenic (+51/+38)	PP_5242/ycaC‑II	GAF domain‑containing sensor histidine kinase/putative hydrolase
Reads supporting (aligned to +/- strand):  ref base G (22/23);  new base A (3/2);  total (25/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-02

GTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTGCGCCAGTCGCGGTGCA  >  NC_002947/5984307‑5984602                                                                                                                                                     |                                                                                                                                                     gTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGGTAAACCGCTCCGACGGTGGGCGGTAggg                                                                                                                                                      >  3:194088/1‑149 (MQ=255)     ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCgg                                                                                                                                                  >  1:19158/1‑149 (MQ=255)     ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCgg                                                                                                                                                  <  8:242995/149‑1 (MQ=255)     ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                                                  <  7:228748/149‑1 (MQ=38)     ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                                                  <  7:139537/149‑1 (MQ=38)       tGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGGCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGt                                                                                                                                                <  5:212761/149‑1 (MQ=255)         gCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGtt                                                                                                                                               <  5:5839/148‑1 (MQ=255)           tCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAAACCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTAc                                                                                                                                            >  4:34950/1‑149 (MQ=255)              ggCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcg                                                                                                                                         >  4:225947/1‑149 (MQ=255)               gCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcgc                                                                                                                                        >  7:100373/1‑149 (MQ=255)                 ccACGGGGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGTTTGCCGTATTCGTGTCAGTCTGCCTTTTAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGAAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGTTTTACCCGCGa                                                                                                                                      <  6:35831/149‑1 (MQ=38)                 ccACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcgcg                                                                                                                                       >  8:291035/1‑148 (MQ=255)                 ccACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcgcg                                                                                                                                       >  5:303300/1‑148 (MQ=255)                         ggCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCa                                                                                                                              <  6:303300/149‑1 (MQ=255)                                 ctggCGCGGGTGGCGATGTTGGTTGTATGCCGTATTCGTGTCAGTCTGCCTTTTAATCAGGAATAGCCTGTGCGGGCCTCTGCGCGGTTAACCCGGCTCCTCGGGGGGGCTTTTGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGt                                                                                                                      <  8:195803/147‑1 (MQ=255)                                        tGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACAt                                                                                                               >  5:77312/1‑148 (MQ=255)                                             tCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAgcg                                                                                                          <  6:77312/148‑1 (MQ=255)                                                       gTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAgcg                                                                                               >  1:257924/1‑149 (MQ=255)                                                              ccGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTa                                                                                        <  7:291035/149‑1 (MQ=255)                                                                    tCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGt                                                                                   <  2:19158/148‑1 (MQ=255)                                                                      gtgtCAGTCGGCCTTTCAAGCACGCATAGCCTGTGCCGGCCTCTGCGCGGGTAAACCCGCTCATACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTtc                                                                                 <  1:135879/148‑1 (MQ=38)                                                                        gtCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCAACGGGCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTtcat                                                                               >  6:282387/1‑148 (MQ=255)                                                                         tCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTtcat                                                                               >  2:45808/1‑147 (MQ=255)                                                                           aGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCGCTCCGCGGGTAAACCCGCTCCTCCGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAg                                                                            <  3:34950/148‑1 (MQ=255)                                                                            gTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGGCAGTACAGGTTT‑ACATCAGCGAGAGGCCAGCGCTGCGTAGCTGTTCATCAGGt                                                                          >  5:150855/1‑149 (MQ=255)                                                                                 ccTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCg                                                                      <  1:45808/148‑1 (MQ=255)                                                                                 ccTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCg                                                                      <  2:257924/148‑1 (MQ=255)                                                                                 ccTTTCAATCACGCATCGCCTGTCCCGCCCCCTGCGCGGTAAACCCCGCCCCTACGGCGGGGTGTGGGGGGGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCgg                                                                     <  4:194088/149‑1 (MQ=255)                                                                                        aTCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTgg                                                              <  3:225947/149‑1 (MQ=255)                                                                                             gCATAGCCTGTGCCGGCCTCTTCGCGGGTAAAACCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTAACCGCGAAGAGGCCAGTACAGGTTT‑AAATAAGCGCGAgg                                                                                                     >  2:103828/1‑105 (MQ=25)                                                                                             gCATAGCCTGTGCCGGCCTCTTCGCGGCTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAgg                                                                                                     <  1:103828/105‑1 (MQ=255)                                                                                                  gcgtgtgCCGGCCTCTTCGGGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTg                                                    <  3:129826/146‑1 (MQ=255)                                                                                                    cTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCg                                                  <  8:100373/149‑1 (MQ=255)                                                                                                          cGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGAcag                                              >  3:116647/1‑147 (MQ=255)                                                                                                          cGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGAcag                                              >  1:47272/1‑147 (MQ=255)                                                                                                                       ggTAAACGCGCTCCTACGGTCGCCTCTAGGGCCGGGATTACCCGCGAAGAGGCCAGTACACGTTT‑AGATCTGCGCGAGGCGATCGCTGCGTAGCTGTTCTTCAGGTTGCGCTAGTAGGGGATACGCTGCGACAGCAGGTTACCGAGccc                               <  6:150855/149‑1 (MQ=255)                                                                                                                             cccGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGc                                                   >  4:103633/1‑123 (MQ=255)                                                                                                                             cccGCCCCTACAGCCGACCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGAt                         >  2:260585/1‑149 (MQ=37)                                                                                                                              ccGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTGACAACACCGCGAGGCCACCGATGCGTAGCTGTTAAAAAGGTTCCGGTATTTGGGCATCGGCTCCGACAGCAGGTTACCCAGCCATTCGAt                         >  1:253051/1‑149 (MQ=255)                                                                                                                              ccGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGa                                                 <  2:179812/124‑1 (MQ=255)                                                                                                                              ccGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGa                                                 >  1:179812/1‑124 (MQ=255)                                                                                                                              ccGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATg                        >  1:131021/1‑149 (MQ=255)                                                                                                                              ccGCCCCTACAGCCGACCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATg                        >  7:7164/1‑149 (MQ=37)                                                                                                                              ccGCCCCTACAGCCGACCGTAGGAGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATg                        >  7:162427/1‑149 (MQ=38)                                                                                                                               cGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGt                       >  5:121666/1‑149 (MQ=255)                                                                                                                                    cTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATg                        >  6:134893/1‑143 (MQ=255)                                                                                                                                    cTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATg                        <  5:134893/143‑1 (MQ=255)                                                                                                                                    cTACGGTCGGCTGTAGGGGAGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTg                  >  2:96291/1‑149 (MQ=255)                                                                                                                                       cGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTgcgc               <  5:282387/149‑1 (MQ=255)                                                                                                                                        ggTCGGCTGTAGGGGCGGGTTTACCCGAGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGATGCGGTAGTTGTGGATAAGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTgcgc               >  4:222550/1‑148 (MQ=255)                                                                                                                                               tGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTGCGCCAGTcgcg       <  6:121666/149‑1 (MQ=255)                                                                                                                                                    gggCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTGCGCCAGTCGCGGTGCa  <  2:47272/149‑1 (MQ=255)                                                                                                                                                     ggCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGtt                   <  6:236678/131‑1 (MQ=255)                                                                                                                                                     ggCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGtt                   >  5:236678/1‑131 (MQ=255)                                                                                                                                                     |                                                                                                                                                     GTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCTGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTT‑ACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGTTGCGCCAGTCGCGGTGCA  >  NC_002947/5984307‑5984602

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: ‑