Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,740,484	T→C	12.0%	intergenic (+49/+22)	hutF → / ← PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,740,484	0	T	C	12.0%	123.1 / 8.4	50	intergenic (+49/+22)	hutF/PP_5037	formiminoglutamate deiminase/lipocalin family lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (22/22);  new base C (4/2);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.22e-01

ATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGA  >  NC_002947/5740337‑5740631                                                                                                                                                     |                                                                                                                                                     aTGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGtt                                                                                                                                                     <  3:278666/149‑1 (MQ=255)  tGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTG‑CACGCGAAGGGCTg                                                                                                                                                    >  4:19698/1‑149 (MQ=38)   ggTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTG‑CACGCGAAGGGCTg                                                                                                                                                    <  3:19698/148‑1 (MQ=38)    gTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAACCCTTCGCGGGCTTG‑CACGCGAAGGGCTgc                                                                                                                                                   <  5:179484/148‑1 (MQ=38)         tGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTg                                                                                                                                                    >  4:333909/1‑142 (MQ=255)         tGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTg                                                                                                                                                    <  3:333909/142‑1 (MQ=255)                   gtggtgCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCaaaa                                                                                                                                    >  5:418315/1‑148 (MQ=255)                         cgcCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAg                                                                                                                            <  3:49634/149‑1 (MQ=255)                          gcCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGCGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCTAAGGGTTGAAACGCAACCCCAAAAA‑ACTCAGt                                                                                                                           <  4:327970/149‑1 (MQ=255)                                            aGGAAGATGAAAGCGGGCGGGCGTTGGCCAAGGTGTTGCGCCAGCTTTTGGGCGGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCt                                                                                                         <  4:313844/149‑1 (MQ=255)                                                      aaGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGacgc                                                                                               >  6:418315‑M2/1‑145 (MQ=255)                                                        gcgggcggGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTGAACCCATACCGGGGAAGCCCCCCCAAGGGTTG‑AACCCAAACCCCAAAA‑AAAAAATGCATTTTTTATATTTTGTTATCGGAcgccc                                                                                             >  2:15111/1‑149 (MQ=255)                                                          gggggggcGTTTGCCATGGTGTTGCGCCAGCTTTTGGGCGGAGCGTACCGGGGTGGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGATGGGTTGAAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgc                                                                                           >  4:298328‑M2/1‑141 (MQ=255)                                                                          aGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTgg                                                                           <  3:289787/149‑1 (MQ=255)                                                                                 gcgcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTgc                                                                                                                                                   >  5:223800/1‑71 (MQ=255)                                                                                 gcgcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTgc                                                                                                                                                   <  6:223800/71‑1 (MQ=255)                                                                                   gcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTTCAGCCCTTAGCGTGCAAG‑CCCGCCAAGGGTTGCAACGCCACCCCAAAAA‑AAGAAGTGGATTTTTTATATTTGGTGATAGGACGCCCGCCACATCAAGCGGCGGGTGTAATaac                                                                  >  6:401799/1‑147 (MQ=255)                                                                                   gcCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTAGCGTGCAAG‑CCCGCGAACGGTTGCAACCCAACCCCAAAAA‑ACTCACTGCAATTTTACTATTTGCGGATCGGACGCCCCCCAGATCAAGCGGAAGGTGTCATAcc                                                                  >  7:386471/1‑149 (MQ=255)                                                                                         ttttGGGCGGAGCGTACCGGGGTGGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCTATGGGTTGAAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCctgct                                                            <  2:361478/149‑1 (MQ=255)                                                                                              ggCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCcg                                                        <  1:113586/148‑1 (MQ=255)                                                                                                   aGCTTACCGGGGTTGCGTTGCAGCCGTGGGCGTGCATC‑CCCGGGAAGGTTTGAAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGcc                                                    <  5:26406/147‑1 (MQ=255)                                                                                                     cGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCt                                                  <  1:82444/147‑1 (MQ=255)                                                                                                                  ctttgcAGCCCTTCGCGTGCAAG‑CCCGCTAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtctc                                   <  2:127287/147‑1 (MQ=255)                                                                                                                  cgttgcAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtctc                                   <  5:401799/149‑1 (MQ=255)                                                                                                                  cgttgcAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTtctc                                   <  1:15111/149‑1 (MQ=255)                                                                                                                   gttgcAGCCCTTGGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTTCTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCTCCCTGGACAGCAGGTTCTCa                                  <  8:386471/149‑1 (MQ=255)                                                                                                                         gCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  8:63228/1‑149 (MQ=255)                                                                                                                         acccTTCGCGGGCTTG‑CACGCGAAGGGCTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  3:264582/2‑149 (MQ=38)                                                                                                                         acccTTCGCGGGCTTG‑CACGCGAAGGGCTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  5:134336/2‑149 (MQ=38)                                                                                                                           ccTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  3:202247/1‑147 (MQ=255)                                                                                                                           ccTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACACCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  3:359135/1‑147 (MQ=255)                                                                                                                           ccTTCGCGGGCTTG‑CACGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTcc                            >  8:234595/1‑147 (MQ=255)                                                                                                                           ccTTCGCGGGCTTG‑CACGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCAGGACAGCAGGTTCTCACGCTcc                            >  2:53415/1‑147 (MQ=39)                                                                                                                            cTTCGCGGGCTTG‑CACGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg                         >  5:118184/1‑149 (MQ=255)                                                                                                                            cTTCGCGGGCTTG‑CACGCGAAGGGCTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAg                         >  2:304780/1‑149 (MQ=39)                                                                                                                             ttCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCACAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATCCCCCTGCTGCCGCGccc                                                   >  2:67209/1‑122 (MQ=255)                                                                                                                             ttCGCGGGCTTG‑CACGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagca                                          >  8:207271/1‑131 (MQ=255)                                                                                                                             ttCGCGGGCTTG‑CACGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGAcagca                                          <  7:207271/131‑1 (MQ=255)                                                                                                                                  gTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCgg                    >  6:126152/1‑148 (MQ=255)                                                                                                                                  gTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCgg                    >  6:199676/1‑148 (MQ=255)                                                                                                                                    gCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccctggcgcaccacccattgcccattcaccatcacatcgcgcacctg                 <  6:7229‑M2/149‑83 (MQ=255)                                                                                                                                    gCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccctgg                                                          <  5:43600‑M2/108‑42 (MQ=255)                                                                                                                                    gCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGacgcccgcccgctttcatcttcctgggcatgccgcccctgg                                                          >  6:43600‑M2/1‑67 (MQ=255)                                                                                                                                     gcttgcacgcgAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAg                 >  6:235274/8‑149 (MQ=255)                                                                                                                                        g‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAATACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGATCCCAGGCCGGCAgtgt              >  1:49069/1‑149 (MQ=255)                                                                                                                                             gagAAGGGTTTCAACTCAACCACAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCTGACGCCCGCCAGAGCAATCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGgtg         <  2:49069/147‑1 (MQ=255)                                                                                                                                              cgATGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGgtgt        <  5:25897/149‑1 (MQ=255)                                                                                                                                              cgAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGgtgt        <  4:202247/149‑1 (MQ=255)                                                                                                                                                tggggTTGCGTTGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGa                                               >  1:290677/3‑108 (MQ=255)                                                                                                                                                tggggTTGCGTTGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGa                                               <  2:290677/106‑1 (MQ=255)                                                                                                                                                    gTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCAGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGa  <  1:53415/149‑1 (MQ=255)                                                                                                                                                     ttGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGa  >  1:396252/1‑148 (MQ=255)                                                                                                                                                     |                                                                                                                                                     ATGGTGAATGGGCAATGGGTGGTGCGCCAGGGGCGGCATGCCCAGGAAGATGAAAGCGGGCGGGCGTTTGCCAAGGTGTTGCGCCAGCTTTTGGGCTGAGCGTACCGGGGTTGCGTTGCAGCCCTTCGCGTGCAAG‑CCCGCGAAGGGTTGCAACGCAACCCCAAAAA‑ACTCAGTGCATTTTTACTATTTGCTGATCGGACGCCCGCCAGATCAAGCGGCTGGTGTCATACCCCTGCTGCCGCGCCCTGGACAGCAGGTTCTCACGCTCCCAGGCCGGCAGTGTCGGTGTGCGCGA  >  NC_002947/5740337‑5740631

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: ‑