Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,941,692	C→T	7.1%	intergenic (+12/+34)	PP_2574 → / ← PP_2575	LysR family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,941,692	0	C	T	7.1%	164.1 / 2.4	56	intergenic (+12/+34)	PP_2574/PP_2575	LysR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (24/28);  new base T (2/2);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.17e-01

ATGCTCGACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCGCGCCGGTCCTGGCGCCGGTCCTG  >  NC_002947/2941549‑2941833                                                                                                                                                |                                                                                                                                               aTGCTCGACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGCCTGCGGCGTGGATGAAGCGAGTCCAGCTGACCAAACCCGCGCACTTGTTAGTGGAGTTTTGTCGGGATGAGCTCGCGAAGTTCCTCAAGTGAGCACGCCATGCCAcccc                                                                                                                                           >  3:172526/1‑149 (MQ=255)     tCGACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCgg                                                                                                                                         >  2:155321/1‑147 (MQ=255)       gACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCa                                                                                                                                       <  1:155321/147‑1 (MQ=255)       gACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAg                                                                                                                                      >  1:210363/1‑148 (MQ=255)              ccGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAg                                                                                                                                      <  1:236452/141‑1 (MQ=255)              ccGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAg                                                                                                                                      >  2:236452/1‑141 (MQ=255)                      gTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCAACCCGGCAGGAGTAGCAtggcgtgg                                                                                                                      >  8:196595/1‑149 (MQ=255)                               tCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCt                                                                                                              >  1:29093/1‑148 (MQ=255)                                 ggggCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAg                                                                                                          >  2:231326/1‑149 (MQ=255)                                   ggctggctGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAggg                                                                                                        <  8:119108/149‑1 (MQ=255)                                   ggctggctGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAggg                                                                                                        <  2:29093/149‑1 (MQ=255)                                       ggctgCGGCGTGGTTGAAGCGAGTCCAGCTGACCACACCGGCCCAGTTGGTCGTGGAGTTTTGTCTGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACACCGGCAGGAGTAGCATGGCGTGTCGATTGCG‑CAtgggat                                                                                                     >  7:85899/1‑146 (MQ=255)                                        gctgCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGa                                                                                                   >  2:72479/1‑149 (MQ=255)                                               cgTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTa                                                                                            <  5:34665/149‑1 (MQ=255)                                                 tGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGc                                                                                          <  3:98534/149‑1 (MQ=255)                                                    ttGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCcgc                                                                                       >  5:234349/1‑149 (MQ=255)                                                     tGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCcgcg                                                                                      >  6:150131/1‑149 (MQ=255)                                                                      aCCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACGTgg                                                                                              <  8:194573/124‑1 (MQ=255)                                                                      aCCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTgg                                                                                              >  7:194573/1‑124 (MQ=255)                                                                      aCCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCCGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGc                                                                     >  4:22817/1‑149 (MQ=255)                                                                       ccAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCt                                                                    <  6:100335/149‑1 (MQ=255)                                                                         aaaCCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGt                                                                  <  1:72479/149‑1 (MQ=255)                                                                         aaaCCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCCGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGt                                                                  <  3:22817/149‑1 (MQ=255)                                                                           aCCGGCGCAGTTGTTCGGGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAg                                                                <  7:219382/149‑1 (MQ=255)                                                                                  cAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTgg                                                         <  2:210363/149‑1 (MQ=255)                                                                                   aGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCTACTCCTGCCGGGGTGGCAtg                                                                                                                            >  4:127585/1‑82 (MQ=25)                                                                                   aGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCTACTCCTGCCGGGGTGGCAtg                                                                                                                            <  3:127585/82‑1 (MQ=25)                                                                                   aGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTgg                                                         >  1:47264/1‑148 (MQ=255)                                                                                   aGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGc                                                        <  8:50253/149‑1 (MQ=255)                                                                                     ttgttCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCTCCAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCa                                                       <  1:206194/149‑1 (MQ=255)                                                                                        ttCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATgg                                                    <  7:80312/148‑1 (MQ=255)                                                                                          cGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTgg                                                         <  3:212949/141‑1 (MQ=255)                                                                                          cGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTgg                                                         >  4:212949/1‑141 (MQ=255)                                                                                             ggAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAggg                                                                                                        <  6:235415/91‑1 (MQ=255)                                                                                             ggAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAggg                                                                                                        >  5:235415/1‑91 (MQ=255)                                                                                              gAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTggg                                             >  2:26416/1‑149 (MQ=255)                                                                                                gTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGtt                                           >  4:146429/1‑149 (MQ=255)                                                                                                 ttttGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAg                                                                <  4:135399/127‑1 (MQ=255)                                                                                                 ttttGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAg                                                                >  3:135399/1‑127 (MQ=255)                                                                                                   ttGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGtttt                                         <  7:196595/148‑1 (MQ=255)                                                                                                    tGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTg                                        <  3:146429/148‑1 (MQ=255)                                                                                                    tGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTg                                        <  2:47264/148‑1 (MQ=255)                                                                                                    tGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGAAGGCACTGGCATGGGCCTGGGTTTTgg                                       <  1:231326/149‑1 (MQ=255)                                                                                                      tCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGcc                                     <  5:150131/149‑1 (MQ=255)                                                                                                        gggAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTc                                   <  6:234349/149‑1 (MQ=255)                                                                                                           aaGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTc                                >  8:88949/1‑149 (MQ=255)                                                                                                                   gCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGtttt                                         <  7:107631/132‑1 (MQ=255)                                                                                                                   gCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGtttt                                         >  8:107631/1‑132 (MQ=255)                                                                                                                             tGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCgcgccggtcctg              >  6:118647/1‑149 (MQ=255)                                                                                                                                    aGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCgcgccggtcctggcgccgg       >  4:254524/1‑149 (MQ=255)                                                                                                                                    aGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGCTTTGGCCTCGTCCTGGTCgcgccggtcctggcgccg        <  7:88949/148‑1 (MQ=255)                                                                                                                                         gCCATGCCACCCCGGCAGGAGTTGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCgcgccggtcctggcgccggtcctg  <  5:215321/149‑1 (MQ=255)                                                                                                                                          ccATGCTACTCCTGCCGGGGTGGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTg                                        <  1:54425/110‑1 (MQ=38)                                                                                                                                          ccATGCTACTCCTGCCGGGGTGGCATGGCGTGGCGATTGCT‑AAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCCCTGTAGGCACTGGCATGGGCCAGGCTTTTg                                        >  2:54425/1‑110 (MQ=25)                                                                                                                                           cATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCgcgccggtcctggcgccg        <  2:31286/141‑1 (MQ=255)                                                                                                                                           cATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCgcgccggtcctggcgccg        >  1:31286/1‑141 (MQ=255)                                                                                                                                                |                                                                                                                                               ATGCTCGACATTGCCGAGCCGGTGGCGCTGTCGGGGCTGGCTGCGGCGTGGTTGAAGCGAGTCCAGCTGACCAAACCGGCGCAGTTGTTCGTGGAGTTTTGTCGGGAAGAGCTGGCGAAGTTCCTGAAGTGAGCACGCCATGCCACCCCGGCAGGAGTAGCATGGCGTGGCGATTGCT‑CAGGGGTTGACCTGGTAGCCGCGCCCTTGCAGGCAACCGCTGTAGGCACTGGCATGGGCCTGGGTTTTGGCCTCGTCCTGGTCGCGCCGGTCCTGGCGCCGGTCCTG  >  NC_002947/2941549‑2941833

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑