Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,623,199	A→G	10.4%	intergenic (+35/‑211)	PP_5517 → / → PP_2295	hypothetical protein/antirestriction protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,623,199	0	A	G	10.4%	124.6 / 5.5	48	intergenic (+35/‑211)	PP_5517/PP_2295	hypothetical protein/antirestriction protein
Reads supporting (aligned to +/- strand):  ref base A (25/18);  new base G (3/2);  total (28/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.74e-01

AGTTCGGGGATGCGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATGGGGTGTCG  >  NC_002947/2623054‑2623341                                                                                                                                                   |                                                                                                                                                aGTTCGGGGATGCGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATc                                                                                                                                              <  5:19558/149‑1 (MQ=255)      ggggATGCGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGc                                                                                                                                          <  6:383446/148‑1 (MQ=255)             cGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCGATTGGGCCCcttga                                                                                                                                   <  4:215923/148‑3 (MQ=255)             cGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAA‑GGGCCCGATTGGGCCCcttgagg                                                                                                                                 <  1:169846/149‑5 (MQ=255)              gtgtGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATc                                                                                                                                              <  8:282402/136‑1 (MQ=255)              gtgtGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATc                                                                                                                                              >  7:282402/1‑136 (MQ=255)               tgtgGAGGTGTTCCAACAGAATGAGTACGCGCTCACCTTCCTTTCTCCGAGTGGTCGGGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTcgc                                                                                                                                <  4:65771/149‑1 (MQ=255)                           ccAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTc                                                                                                                     >  6:68631/1‑148 (MQ=255)                            cAACAGACTGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGGCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTc                                                                                                                                  <  5:134781/134‑1 (MQ=255)                            cAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATAAGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGa                                                                                                                   >  8:160643/1‑149 (MQ=255)                            cAACAGAATGAGTACGCGGTAACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACAACTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATAAGCAATCACACCTCAAGGTGCCCAATCGGGACCTTTTTc                                                                                                                                  >  6:134781/1‑134 (MQ=255)                                              gTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAgg                                                                                                >  8:160154/1‑149 (MQ=255)                                                      ccttTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGc                                                                                        >  2:286262/1‑149 (MQ=255)                                                       cttTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGcc                                                                                       <  8:89205/149‑1 (MQ=255)                                                        tttCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACGTAAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGcc                                                                                       >  1:107635/1‑149 (MQ=255)                                                            tcCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACa                                                                                  <  7:160643/149‑1 (MQ=255)                                                             ccGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGa                                                                                    >  6:320528/1‑146 (MQ=255)                                                                         gCCTTCTACACCTACACCAAGTTCGTGAGCAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCCTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGa                                                                     <  5:5630/149‑1 (MQ=255)                                                                          ccTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGaa                                                                    <  1:286262/149‑1 (MQ=255)                                                                            ttCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAgc                                                                  >  4:75701/1‑149 (MQ=255)                                                                             tCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGGCGAGTCTGGAG‑AATTCGCAGGGGCTACGCCCGACAGAAGCCGCGTAGAcgcg                                                                 >  4:19949/1‑149 (MQ=255)                                                                                 cacctacaccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAgcgc                                                                <  3:75701/146‑1 (MQ=255)                                                                                    ctacaccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGga                                                                                                            <  4:130476/100‑1 (MQ=255)                                                                                    ctacaccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGga                                                                                                            >  3:130476/1‑100 (MQ=255)                                                                                    ctacaccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCaa                                                           >  8:213071/1‑148 (MQ=255)                                                                                    ctacaccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACACAATCCGCGTAGAAGCGCGCCaa                                                           >  3:47136/1‑148 (MQ=255)                                                                                        accAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCGAATCGGGGGCTTTTTGGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTACGCCCGACTGATTCCGCGTAGGAGCGCGGCAAAAt                                                        >  6:188885/1‑147 (MQ=255)                                                                                         ccAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTAc                                                     <  5:68631/149‑1 (MQ=255)                                                                                          cAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTAc                                                     >  7:156196/1‑148 (MQ=255)                                                                                                                     aGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGaa                          <  7:160154/149‑1 (MQ=255)                                                                                                                      gTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGaaa                         <  7:213071/149‑1 (MQ=255)                                                                                                                             gCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCcgc                                                                          <  5:3665/93‑1 (MQ=255)                                                                                                                             gCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCcgc                                                                          >  6:3665/1‑93 (MQ=255)                                                                                                                             gCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCa                  <  2:107635/149‑1 (MQ=255)                                                                                                                                aTCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACt                <  1:151816/148‑1 (MQ=255)                                                                                                                                aTCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACt                >  2:151816/1‑148 (MQ=255)                                                                                                                                     acCTCAAGGGGCCCAATCGGGCCGTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGGAGCGCGCCAAAATTACGAAAACACGTCATTTCCGCAAATGGTCTTAAATCACTGGCATg          >  8:156620/1‑149 (MQ=255)                                                                                                                                     acCTCAAGGGGCCCAATCGAGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGaaaa                                                >  6:159997/1‑111 (MQ=255)                                                                                                                                     acCTCAAGGGGCCCAATCGAGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGaaaa                                                <  5:159997/111‑1 (MQ=255)                                                                                                                                       gaaaaagggCCCGATTGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATggg        >  7:170383/7‑149 (MQ=255)                                                                                                                                       gaaaaagggCCCGATTGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATggg        >  5:93125/7‑149 (MQ=255)                                                                                                                                        tCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAGAAATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATggg        >  1:279322/1‑149 (MQ=255)                                                                                                                                        tCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATgggg       >  7:213724/1‑149 (MQ=255)                                                                                                                                        tCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATgggg       >  3:58698/1‑149 (MQ=255)                                                                                                                                         aaaagggCCCGATTGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATGGGgt      >  1:162582/5‑149 (MQ=255)                                                                                                                                           aGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTGGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCGACAAATGGAAAGAAGTGAGTTGCAGGGGgtgg    >  8:53435/1‑148 (MQ=255)                                                                                                                                           aGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATGGGgtgt    >  8:278274/1‑149 (MQ=255)                                                                                                                                             gggCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAGATAAATCACTTGCAGGGGGTGTCg  >  6:18312/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                                AGTTCGGGGATGCGTGTGGAGGTGTTCCAACAGAATGAGTACGCGGTCACCTTCCTTTCTCCGAGTGGTCGAGCCTTCTACACCTACACCAAGTTCGTGAGGAAGCGCTGACG‑CAAGTCATACGCAATCACACCTCAAGGGGCCCAATCGGGCCCTTTTTCGCGTCTGTACGTCGATTCTGGAG‑AATTCGCAGGGGCTAAGCCCGACAGAATCCGCGTAGAAGCGCGCCAAAATTACGAAAACACGTCATTTCCACAAATGGAAATAAATCACTTGCATGGGGTGTCG  >  NC_002947/2623054‑2623341

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: ‑