Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,984,436	T→C	15.5%	intergenic (+32/+57)	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	5,984,436	0	T	C	15.5%	83.8 / 8.9	43	intergenic (+32/+57)	PP_5242/ycaC‑II	GAF domain‑containing sensor histidine kinase/putative hydrolase
Reads supporting (aligned to +/- strand):  ref base T (15/17);  new base C (3/3);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.17e-01

TGGGCTTGGCGATCTGTAGTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGT  >  NC_002947/5984289‑5984584                                                                                                                                                     |                                                                                                                                                     tGGGCTTGGCGTTCTGTAGTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑TGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTc                                                                                                                                                     <  5:80843/149‑1 (MQ=255)    gcctGGCGATCGTTAGTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGTTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTCTGCCGGCCTCTTCGCGGTTAAACCCGCTCCTa                                                                                                                                                  <  8:182764/146‑1 (MQ=255)    gCTTGGCGATCTGTAGTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTa                                                                                                                                                  <  7:139832/149‑1 (MQ=255)                    ttCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTa                                                                                                                                                  >  1:199902/1‑133 (MQ=255)                    ttCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTa                                                                                                                                                  <  2:199902/133‑1 (MQ=255)                    ttCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACg                                                                                                                                                <  5:63568/135‑1 (MQ=255)                    ttCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACg                                                                                                                                                >  6:63568/1‑135 (MQ=255)                    ttCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAgggg                                                                                                                                  >  6:306742/1‑149 (MQ=255)                       ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCgg                                                                                                                               >  5:292620/1‑149 (MQ=255)                       ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                               <  2:272570/149‑1 (MQ=38)                       ggTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAAACCGCGCCGACGGGCGGGGGGAGgggggg                                                                                                                               >  8:16786/1‑149 (MQ=255)                             tCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAgg                                                                                                                                    >  6:100914/1‑138 (MQ=255)                             tCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAgg                                                                                                                                    <  5:100914/138‑1 (MQ=255)                             tCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCACTTAGCGGGGTAACCCGCGCCTAAAGGGGGGTGTTGGGGCGGGgtttc                                                                                                                         >  5:35532/1‑147 (MQ=255)                                 gCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcgc                                                                                                                     <  7:104812/149‑1 (MQ=255)                                   ccACGGCGGGCAGCTGCAGGCGCTGGGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAggg                                                                                                                                   >  1:3807/1‑134 (MQ=255)                                   ccACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAggg                                                                                                                                   <  2:3807/133‑1 (MQ=255)                                   ccACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCcgcg                                                                                                                    >  7:98717/1‑148 (MQ=255)                                   ccACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                               <  5:181345/137‑1 (MQ=37)                                   ccACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                               >  6:181345/1‑137 (MQ=37)                                      cggcggGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCATGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCAGTAGGGGCGGGTTTACCCGCGAaga                                                                                                                >  1:93148/1‑149 (MQ=255)                                                  gCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                               <  4:64306/122‑1 (MQ=25)                                                  gCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCgg                                                                                                                               >  3:64306/1‑122 (MQ=25)                                                    agggggt‑GGTGTCGAAGTTGGGTGTAGGCCTGATTCTTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCGCTTGGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGtt                                                                                                  <  6:126859/143‑1 (MQ=37)                                                        gcT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTACTGGCCTCTTCGCGGGTAAACCCGCCCCTACAGCCGACCGTAGGAGCGGGTTTACCCGCGAAGAGGCCGGCACAggctatgc                                                                                              >  1:41855/1‑143 (MQ=17)                                                             gtgtCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCa                                                                                           <  5:306742/148‑1 (MQ=255)                                                              tgtCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCGGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAgc                                                                                         <  6:292620/149‑1 (MQ=255)                                                               gtCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGa                                                                                                                   <  7:257272/122‑1 (MQ=255)                                                               gtCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGa                                                                                                                   >  8:257272/1‑122 (MQ=255)                                                                tCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTATTCGCGGGTAAAAACGCAACTACCGACCGCGGTAGGGGCGGGTTTAACCCCCAATACGCCACTTCACGTTTAAATCAgcg                                                                                        >  8:43682/1‑148 (MQ=255)                                                                      ttGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTAc                                                                                                                         >  5:242523/1‑109 (MQ=255)                                                                      ttGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTAc                                                                                                                         <  6:242523/109‑1 (MQ=255)                                                                        gggTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAg                                                                               >  4:130668/1‑149 (MQ=255)                                                                                             cAGTCTGCCTTTGTATCACGCATAGCCTGTGCCGTCCTCTTCGCGGGTAAACCCGCTCCTTCGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTtcatca                                                           <  7:43682/148‑1 (MQ=255)                                                                                                  tGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAAACCGCAACTAAGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGc                                                     >  1:84608/1‑149 (MQ=255)                                                                                                    ccTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCgg                                                   >  7:33710/1‑149 (MQ=255)                                                                                                         gAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGtt                                              >  5:138018/1‑149 (MQ=255)                                                                                                           aTCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTgg                                            >  1:37486/1‑149 (MQ=255)                                                                                                                gCATAGCCTGTGCCGGCCTCTTCGCGGGTAAAACCGCACCGACGGGCGGGTGTAGGGGCGGGTGTACACGCGGAGAGGCCAGTACAGGTTTAAATGAGCGCCGGGCCAGCGGGGGGGAGCGGTGGAGGCGGGTGCGGTAGTTGGGGaga                                       >  6:309155/1‑147 (MQ=16)                                                                                                                            ccGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGAcag                            <  3:130668/148‑1 (MQ=255)                                                                                                                             cGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGAcagca                          <  8:98717/149‑1 (MQ=255)                                                                                                                                      cgcgGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTAccc                  <  2:37486/148‑1 (MQ=255)                                                                                                                                               aCCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGa        >  3:128059/1‑149 (MQ=255)                                                                                                                                                     tCCTACGGTCGGCTGTAGGGCCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCCAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGt  >  5:219519/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                     TGGGCTTGGCGATCTGTAGTTCGGTGGCTCAGGCCCACGGCGGGCAGCTGCAGGCGCT‑GGTGTCGCAGTTGGGTGGATGCCGGATTCGTGTCAGTCTGCCTTTGAATCACGCATAGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGTCGGCTGTAGGGGCGGGTTTACCCGCGAAGAGGCCAGTACAGGTTTACATCAGCGCGAGGCCAGCGCTGCGTAGCTGTTCATCAGGTTGCGGTAGTTGGGGATACGCTGCGACAGCAGGTTACCCAGCCCTTCGATGTCGT  >  NC_002947/5984289‑5984584

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: ‑