Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,430,404	Δ1 bp	8.5%	intergenic (‑86/+75)	PP_4769 ← / ← PP_4770	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,430,404	0	T	.	8.5%	143.6 / 7.6	47	intergenic (‑86/+75)	PP_4769/PP_4770	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (18/25);  new base . (2/2);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.60e-01

GTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCT  >  NC_002947/5430256‑5430552                                                                                                                                                        |                                                                                                                                                     gTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGt                                                                                                                                                      <  5:64631/149‑1 (MQ=255)  tGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                                     <  4:258021/149‑1 (MQ=255)  tGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                                     <  7:21039/149‑1 (MQ=255)      ccTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACAcc                                                                                                                                                 <  1:37723/149‑1 (MQ=255)           cgcACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTgg                                                                                                                                            <  7:113140/149‑1 (MQ=255)            gcACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTggg                                                                                                                                           >  6:287528/1‑149 (MQ=255)                 gtgtAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCgg                                                                                                                                      <  2:265932/149‑1 (MQ=255)                    tagtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCg                                                                                                                                   >  5:324193/1‑149 (MQ=255)                      gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGt                                                                                                                                  <  4:174666/148‑1 (MQ=37)                      gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGt                                                                                                                                  <  5:287528/148‑1 (MQ=255)                      gtagAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTg                                                                                                                                 >  5:215460/1‑149 (MQ=255)                                  cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAgg                                                                                                                       <  3:84308/147‑1 (MQ=255)                                  cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAg                                                                                                                        <  6:324193/146‑1 (MQ=255)                                  cacaTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCCCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAgggg                                                                                                                     >  8:74470/1‑149 (MQ=255)                                    caTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                                     >  3:113479/1‑115 (MQ=255)                                    caTCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTa                                                                                                                                                     <  4:113479/115‑1 (MQ=255)                                              cAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑GGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGccc                                                                                                         <  8:42274/149‑1 (MQ=255)                                                   cgATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCgg                                                                                                     >  3:287943/1‑148 (MQ=255)                                                      tCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAAt                                                                                                 >  7:251165/1‑149 (MQ=255)                                                        tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                               >  3:121089/1‑149 (MQ=255)                                                        tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                               >  8:42091/1‑149 (MQ=255)                                                        tttttCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGc                                                                                               >  1:17157/1‑149 (MQ=255)                                                            tCACCTGGGAACCTCATTTTTGGCCTGGAGTACCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCcag                                                                                            >  5:203425/1‑148 (MQ=255)                                                              acgtGGGAACGTGATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTTGCGGACACGCCCGCTCGCACAGGTAT‑CGCGCGTACAGCCGTGGGAGCGGGCGTGccc                                                                                                                              <  2:279581/109‑1 (MQ=255)                                                              aCCTGGGAACCTCATTTTTGGACTGGAGTTCAGGGGGGC‑TGCTGCGCAGAACATTCCCGGACACGCCCCCTCCCACAGGTAT‑CGCGCGTACACACTTTGGAGCGGGCGTcccc                                                                                                                              >  1:279581/1‑113 (MQ=255)                                                                   ggAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACCCCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTAt                                                                                      <  8:310025/147‑1 (MQ=255)                                                                   ggAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGc                                                                                    <  1:165899/149‑1 (MQ=255)                                                                        cTCATTTTTGGCCTGGAGTGCCGGGGGGCTTGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGa                                                                                >  1:225937/1‑149 (MQ=255)                                                                          cATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCt                                                                             >  4:260531/1‑149 (MQ=255)                                                                           aTTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCt                                                                             <  6:124229/148‑1 (MQ=255)                                                                            tttttGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGt                                                                           <  6:215460/149‑1 (MQ=255)                                                                                  gCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGAc                                                                      <  2:54655/148‑1 (MQ=255)                                                                                    cTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGt                                                                    >  6:140924/1‑148 (MQ=255)                                                                                        aGTGCCGAGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGaa                                                               <  4:131566/149‑1 (MQ=255)                                                                                             cGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAtcgtc                                                          <  4:121089/149‑1 (MQ=255)                                                                                             cGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAtcgtc                                                          <  7:42091/149‑1 (MQ=255)                                                                                                                           acacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTTGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                              <  3:260531/149‑1 (MQ=255)                                                                                                                           acacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                              <  1:102600/149‑1 (MQ=255)                                                                                                                           acacGCCCGCTCCCACAGGTAT‑CGCGAGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTg                              <  7:74470/149‑1 (MQ=255)                                                                                                                            cacGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGc                             <  1:262537/149‑1 (MQ=255)                                                                                                                               gCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCa                           >  1:193350/1‑148 (MQ=255)                                                                                                                                 ccGCTCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCaaaa                        >  6:299372/1‑149 (MQ=37)                                                                                                                                     tCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAt                                                              >  6:36430/1‑107 (MQ=21)                                                                                                                                     tCCCACGGGTGTACGCGCG‑ATACCTGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAAt                                                              <  5:36430/107‑1 (MQ=21)                                                                                                                                       ccACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCg                  >  7:294305/1‑149 (MQ=255)                                                                                                                                       ccACAGGTAT‑CGCGCGTACACCCGTCGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCg                  >  4:110137/1‑149 (MQ=255)                                                                                                                                                t‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGAAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTAt         <  4:287943/149‑1 (MQ=255)                                                                                                                                                      cgTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGcc    <  8:251165/149‑1 (MQ=255)                                                                                                                                                        tACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCt  <  2:225937/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                     GTGGGCCTGGCGCACGGTGTAGTAGAGGTTCTGCACATCGGCGAACAGCGCGATCTTTTTCACCTGGGAACCTCATTTTTGGCCTGGAGTGCCGGGGGGC‑TGCTGCGCAG‑ACCTTCGCGGACACGCCCGCTCCCACAGGTAT‑CGCGCGTACACCCGTGGGAGCGGGCGTGCCCGCGAAGGGGCGCAAAGCGCCCCCGGAAATGCCAGCAGTATGCCAGACCTGTCAGACGTAAGAATCGTCGTCCGAGAAGAACCCACCGTCATCGCTGCCAAAACCACCGTCGGCGTATCCGCCCT  >  NC_002947/5430256‑5430552

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: ‑