Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,819,796	T→C	9.6%	intergenic (+33/‑442)	rpoS → / → PP_1624	RNA polymerase sigma S factor/group II intron‑encoding maturase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,819,796	0	T	C	9.6%	146.1 / 5.6	52	intergenic (+33/‑442)	rpoS/PP_1624	RNA polymerase sigma S factor/group II intron‑encoding maturase
Reads supporting (aligned to +/- strand):  ref base T (22/25);  new base C (3/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 6.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01

CTGGAGATCGGCCTTACCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAGGCAAGGGTGTCGCGGGT  >  NC_002947/1819650‑1819944                                                                                                                                                    |                                                                                                                                                      cTGGAGATCGGCCTTACCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCg                                                                                                                                                     >  7:215298/1‑149 (MQ=255)  tGGAGATCGGCCTTACCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCgg                                                                                                                                                    <  5:270713/149‑1 (MQ=255)       aTCGGCCTTACCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑t                                                                                                                                              >  1:13537/1‑149 (MQ=255)                aCCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTtgtgt                                                                                                                                      <  8:62717/148‑1 (MQ=255)                aCCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTtgtgt                                                                                                                                      <  6:201869/148‑1 (MQ=255)                aCCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTtgtgt                                                                                                                                      >  7:62717/1‑148 (MQ=255)                aCCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCC‑GAGATCACCGGGGCG‑ttttttgt                                                                                                                                       <  8:29707/147‑4 (MQ=255)                  ccGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTgcg                                                                                                                                   >  6:248346/1‑149 (MQ=255)                        aCGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCTAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGc                                                                                                                             <  8:231728/149‑1 (MQ=255)                               cGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGgcgc                                                                                                                      >  2:42457/1‑149 (MQ=255)                               cGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGgcgc                                                                                                                      >  3:80621/1‑149 (MQ=255)                                      tCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTgcgc                                                                                                               <  2:96090/149‑1 (MQ=255)                                              gAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATgcg                                                                                                        <  8:215298/148‑1 (MQ=255)                                                                cgcgAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTgtgg                                                                                      <  6:254410/148‑1 (MQ=255)                                                                 gcgAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTtgtg                                                                                       >  7:178822/1‑146 (MQ=255)                                                                 gcgAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTtgtg                                                                                       <  8:178822/146‑1 (MQ=255)                                                                  cgAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGtggtgg                                                                                   <  4:77419/149‑1 (MQ=255)                                                                          ttGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑ttt                                                                                                                                            <  7:104559/84‑1 (MQ=255)                                                                          ttGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑ttt                                                                                                                                            >  8:104559/1‑84 (MQ=255)                                                                          ttGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTgg                                                                           >  3:299369/1‑149 (MQ=255)                                                                             aaaaGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCAGCTTGGTTGTGGTGGCCAAGTGGGt                                                                         >  5:152780/1‑148 (MQ=255)                                                                              aaatattGGTCTGTCCAGCGAGTCATTGTTCCAGAAGCTACCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGa                                                                       <  8:189073/143‑1 (MQ=255)                                                                              aaaGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGa                                                                       <  5:248346/149‑1 (MQ=255)                                                                              aaaGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGa                                                                       >  5:45525/1‑149 (MQ=255)                                                                               aaGAATGGTCTGTCCATCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTCATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCAGCTTGATTGTCGTGGCCAAGAGGGTGa                                                                       >  2:255454/1‑148 (MQ=25)                                                                                aGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACt                                                                     <  6:136657/149‑1 (MQ=255)                                                                                   aTGGTCTGTCCAGCGAGTCATTGTTCAAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTgg                                                                  <  6:5540/149‑1 (MQ=255)                                                                                      gTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCTGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAgg                                                               <  4:70380/149‑1 (MQ=255)                                                                                      gTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAgg                                                               <  5:209325/149‑1 (MQ=255)                                                                                      gTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAgg                                                               >  6:187763/1‑149 (MQ=255)                                                                                        cTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGt                                                              >  4:205539/1‑148 (MQ=255)                                                                                           tCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGaaa                                                          <  5:187763/149‑1 (MQ=255)                                                                                                 gAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCctc                                                    <  6:152780/149‑1 (MQ=255)                                                                                                            ccAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCgg                                         >  7:93739/1‑149 (MQ=255)                                                                                                              aGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGc                                        >  7:219996/1‑148 (MQ=255)                                                                                                               gTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTaca                                                >  2:107857/1‑139 (MQ=255)                                                                                                               gTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTaca                                                <  1:107857/139‑1 (MQ=255)                                                                                                                tagctagcGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAg                                     >  4:65399/1‑149 (MQ=255)                                                                                                                  gctagcGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAggg                                   <  2:13537/149‑1 (MQ=255)                                                                                                                      gcgcTGTAACAAATTACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGaa                                <  1:255454/148‑1 (MQ=255)                                                                                                                        gcTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAgt                              <  8:264686/148‑1 (MQ=255)                                                                                                                              aCAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTTTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGcc                       >  2:49842/1‑149 (MQ=255)                                                                                                                                aaaaaaCGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCg                      >  8:172568/1‑148 (MQ=255)                                                                                                                                aaaaaaCGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGGGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCgg                     >  5:7575/1‑149 (MQ=255)                                                                                                                                 aaaaaCGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCg                      >  7:285434/1‑147 (MQ=255)                                                                                                                                 aaaaaCGCCCC‑GAGATCACCGGGGCGTTTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAACGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCg                      >  1:124118/1‑148 (MQ=11)                                                                                                                                 aaaaaCGCCCC‑GAGATCACCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTtgtg                                                                                       <  2:147353/82‑1 (MQ=14)                                                                                                                                 aaaaaCGCCCC‑GAGATCACCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTtgtg                                                                                       >  1:147353/1‑82 (MQ=14)                                                                                                                                 aaaaaCGCCCC‑GAGATCACCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCg                      >  3:150032/1‑147 (MQ=11)                                                                                                                                  aaaaCGACCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAg                   <  3:163648/149‑1 (MQ=255)                                                                                                                                       gCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAGGCAAg              <  1:42457/149‑1 (MQ=255)                                                                                                                                        ccccGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAGGCAAgg             <  4:299369/149‑1 (MQ=255)                                                                                                                                                    tcGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAGGCAAGGGTGTCGCGGGt  >  2:193609/1‑149 (MQ=34)                                                                                                                                                    |                                                                                                                                                      CTGGAGATCGGCCTTACCCGTGAACGGGTGCGGCAAATCCAGGTGGAAGGGCTCAAGCGCTTGCGCGAGATCCTTGAAAAGAATGGTCTGTCCAGCGAGTCATTGTTCCAGTAGCTAGCGCTGTAACAAAAAACGCCCCGGTGATC‑TCGGGGCG‑TTTTTGTGTGCGCCAGGCATGGCGCGTTGCGCGTATGCGCAACCCGCTTGGTTGTGGTGGCCAAGTGGGTGACTTGGAGGTGAAAGTCCTCTACACACCCGGCAAGGGGAAGTGTTAGCCGGAGGCAAGGGTGTCGCGGGT  >  NC_002947/1819650‑1819944

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: ‑