Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,041,393	G→A	9.1%	intergenic (‑59/‑125)	PP_0900 ← / → colR	PAP2 family protein/two‑component system response regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,041,393	0	G	A	9.1%	117.9 / 2.5	44	intergenic (‑59/‑125)	PP_0900/colR	PAP2 family protein/two‑component system response regulator
Reads supporting (aligned to +/- strand):  ref base G (21/19);  new base A (2/2);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.62e-01

CTCCAGCAGGATCAAGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTCTTTTGGTTG  >  NC_002947/1041245‑1041536                                                                                                                                                      |                                                                                                                                                   cTCCAGCAGGATCAAGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCg                                                                                                                                                    <  3:29881/149‑1 (MQ=255)           aTCAAGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCa                                                                                                                                          <  5:129501/149‑1 (MQ=255)              aaGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGt                                                                                                                                        >  8:69163/1‑148 (MQ=255)               aGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTg                                                                                                                                       >  1:327678/1‑148 (MQ=255)                   cACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGaaaa                                                                                                                                   >  5:4691/1‑148 (MQ=255)                      cGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAAcc                                                                                                                               >  2:316229/1‑149 (MQ=255)                         aGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTAACCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTc                                                                                                                            <  1:232013/149‑1 (MQ=255)                             gCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGt                                                                                                                        <  2:303702/149‑1 (MQ=255)                                   tgAATCACCATGTACATTCAGTAGTTGATAGGGCGAGGGCTTGTGCGTTTCTGGATGACTGCTCAATGGCGTGAAAAAGATCGGGCATTGTCTACCGCCCGCTATCCTGTG‑TCAGTGAAGGATCAGTGAAAAAACCGTCAAGTTCGGt                                                                                                                   <  8:263395/147‑1 (MQ=255)                                     aaTCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCTCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGa                                                                                                                 >  7:263395/1‑148 (MQ=255)                                     aaTCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGaa                                                                                                                <  2:147506/149‑1 (MQ=255)                                       tCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAAtt                                                                                                              >  4:127634/1‑149 (MQ=255)                                          ccAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTc                                                                                                           <  5:321825/149‑1 (MQ=255)                                                      agtagtTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTgg                                                                                                >  4:183530/1‑148 (MQ=255)                                                               tCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAg                                                                                      <  2:109855/149‑1 (MQ=255)                                                                                    gctgcATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTgcgc                                                               <  1:316229/148‑1 (MQ=255)                                                                                    gctgcATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGcc                                                              >  3:38057/1‑149 (MQ=255)                                                                                        cATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTGAGCCGGGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGc                                                           >  1:284909/1‑149 (MQ=255)                                                                                         aTGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCcg                                                         <  1:144170/149‑1 (MQ=255)                                                                                                   cAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                <  4:38057/148‑1 (MQ=255)                                                                                                    aGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGc                                              <  7:69163/149‑1 (MQ=255)                                                                                                       gcgcGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                <  8:197398/144‑1 (MQ=255)                                                                                                       gcgcGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                >  7:197398/1‑144 (MQ=255)                                                                                                                 gATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGca                                 >  2:353782/1‑149 (MQ=255)                                                                                                                 gATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACAGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCATCACAGCGAGAAGCGCCGca                                 >  3:91452/1‑149 (MQ=255)                                                                                                                   tCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGca                                 >  7:108991/1‑147 (MQ=255)                                                                                                                     gggCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAg                              <  1:353782/148‑1 (MQ=255)                                                                                                                     gggCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAg                              <  5:308929/148‑1 (MQ=255)                                                                                                                     gggCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAg                              >  6:308929/1‑148 (MQ=255)                                                                                                                      ggCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCg                                             >  3:61526/1‑132 (MQ=255)                                                                                                                      ggCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCg                                             <  4:61526/132‑1 (MQ=255)                                                                                                                           tGTCGACCGCCCGCTATCCTGTG‑TCCATGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                >  8:158551/1‑124 (MQ=255)                                                                                                                           tGTCGACCGCCCGCTATCCTGTG‑TCCATGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                <  7:158551/124‑1 (MQ=255)                                                                                                                           tGTCGACCGCCCGCTATCCTGTG‑TCCATGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                >  6:87080/1‑124 (MQ=255)                                                                                                                           tGTCGACCGCCCGCTATCCTGTG‑TCCATGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACcaca                                                <  5:87080/124‑1 (MQ=255)                                                                                                                            gTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAAc                       <  3:183530/148‑1 (MQ=255)                                                                                                                                aCCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATg                  >  8:107964/1‑149 (MQ=255)                                                                                                                                 ccgcgctcTATCCTGTG‑TCCGTGATGGAGCAGTGAAAAAACCGTCAAGTGCGGGGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATgc                 <  6:4691/149‑1 (MQ=255)                                                                                                                                    cggtctttCCTTTG‑TCAGTGAAGGATCAGTGATATAACCGTCAAGTGCGGTGAATTTTACCCAGGGCTGGCAGCGTGCAGTCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGGGCAGCACAGCGAGAAGCGCCGATGAGGAGAAAcc                      <  8:187944/134‑1 (MQ=255)                                                                                                                                    cccgcTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAAca                      >  7:187944/1‑140 (MQ=255)                                                                                                                                      cgcTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCAtt            >  4:352896/1‑149 (MQ=255)                                                                                                                                      cgcTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCAt             >  1:161179/1‑148 (MQ=255)                                                                                                                                       gcTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTc           <  3:127634/149‑1 (MQ=255)                                                                                                                                       gcTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTc           >  4:23131/1‑149 (MQ=255)                                                                                                                                         tATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTCtt         >  7:319139/1‑149 (MQ=255)                                                                                                                                                      gTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCAAGGGAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTCTTTTGGTTg  >  1:293938/1‑147 (MQ=255)                                                                                                                                                      |                                                                                                                                                   CTCCAGCAGGATCAAGGCCACCGCAGTCGCCAGGGGAATCCCCAGGTACAGCCAGTAGTTGATCGGGCGAGGGCGGGTGCGTTGCTGCATGACGGCTCCAGGGCGCGAAAAAGATCGGGCATTGTCGACCGCCCGCTATCCTGTG‑TCCGTGAAGGATCAGTGAAAAAACCGTCAAGTGCGGTGAATTTTCCCCAGGGCTGGCACCGTGCAGGCA‑‑‑TAGGCCTTAAGCTGCGCCTGCCGCGCACCACAGCGAGAAGCGCCGCACAGGAGAAACCGATGCGCATTCTTTTGGTTG  >  NC_002947/1041245‑1041536

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: ‑