Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,511,112	T→A	17.9%	pseudogene (497/1851 nt)	PP_1325 ←	putative lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,511,112	0	T	A	17.9%	63.3 / 8.6	28	pseudogene (497/1851 nt)	PP_1325	putative lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (14/9);  new base A (2/3);  total (16/12)
Fisher's exact test for biased strand distribution p-value = 6.24e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

TGCTCCAGGGTGCCGGCGCTTTTCACGGCGAAGGCCAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGTTCGGCGAGGCGCTGCAGGCTGG  >  NC_002947/1510968‑1511253                                                                                                                                                 |                                                                                                                                              tgctCCAGGGTGCCGGCGCTTTTCACGGCGAAGGCCAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCGAGATGGCGTCATTGTTGGTGCTGGCGGCCTGgccg                                                                                                                                          >  2:36132/1‑150 (MQ=255) tgctCCAGGGTGCCGGCGCTTTTCACGGCGAAGGCCAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGgccg                                                                                                                                          >  1:627558/1‑150 (MQ=255)       aGGGTGCCGGCGCTTTTCACGGCGAAGGCCAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCAGGCCGCCagca                                                                                                                                    <  1:103125/150‑4 (MQ=255)                                    cAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGAt                                                                                                                   <  2:664804/138‑1 (MQ=255)                                    cAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGAt                                                                                                                   >  1:664804/1‑138 (MQ=255)                                      tgcggggccagccagccagGGTCTGACCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCgg                                                                                                     <  1:464149/143‑1 (MQ=255)                                       gCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGc                                                                                                    >  2:734391/1‑150 (MQ=255)                                             ccagccagccagGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAg                                                                                              <  2:736124/150‑1 (MQ=255)                                              cagccagccagGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAgg                                                                                             <  1:734391/150‑1 (MQ=255)                                                                            tgctgcAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCCGCCTGTCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCACCGGCTTCGAGCgcggcggcg                                                               >  2:124166/1‑150 (MQ=255)                                                                                 cAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGcac                                                          >  2:159739/1‑150 (MQ=255)                                                                                   gTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCacac                                                        >  1:490650/1‑150 (MQ=255)                                                                                        tctGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAg                                                   >  2:112030/1‑150 (MQ=255)                                                                                        tctGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAg                                                   >  2:507429/1‑150 (MQ=255)                                                                                              ggcagCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTgcgc                                             <  2:111528/150‑1 (MQ=255)                                                                                               gcagCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTgcgcg                                            >  1:557318/1‑150 (MQ=255)                                                                                                            cAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGc                               >  2:6489/1‑150 (MQ=255)                                                                                                             aaGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAg                                                   <  1:73672/129‑1 (MQ=255)                                                                                                             aaGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAg                                                   >  2:73672/1‑129 (MQ=255)                                                                                                                 cccAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCa                          <  1:112030/150‑1 (MQ=255)                                                                                                                   cAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGt                        <  2:490650/150‑1 (MQ=255)                                                                                                                                       cttGGCGGCCAGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGTTCGGCGAGGCGCTGCAgg      >  2:115076/3‑148 (MQ=255)                                                                                                                                       cttGGCGGCCAGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGTTCGGCGAGGCGCTGCAgg      <  1:115076/146‑1 (MQ=255)                                                                                                                                        ttGGCGGCCAGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCa                                                                                    <  2:543375/68‑1 (MQ=255)                                                                                                                                        ttGGCGGCCAGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCa                                                                                    >  1:543375/2‑69 (MQ=255)                                                                                                                                         tGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGTTCGGCGAGGCGCTGCAGGCTgg  >  2:458492/1‑150 (MQ=255)                                                                                                                                              gcCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGt                                                 >  2:548542/1‑98 (MQ=255)                                                                                                                                              gcCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGt                                                 <  1:548542/98‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                              TGCTCCAGGGTGCCGGCGCTTTTCACGGCGAAGGCCAGGCTGGTCCAGCCAGCCAGGGTCTGATCGTTGGTTGGCTGCTGCAGTTGCTCTGCAGGCAGCGAGGCGACCAAGGCCCAGATGGCGTCATTGTTGGTGCTGGCGGCCTGGCCGCCAAGCAGCGGGGCCAGCAGGATGCGCTGCTGTGCGGCAGCCAGGGCCTGGCCATCGGCTTCGAGCGCGGCGGCGTGCACACTGTAGGTGCGCGCTTGCAGGTCTGCCGGCAGTTCGGCGAGGCGCTGCAGGCTGG  >  NC_002947/1510968‑1511253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑