Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	4,740,819	2 bp→CT	intergenic (+56/+696)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,740,819	0	T	C	97.6%	125.2 / ‑5.4	41	intergenic (+56/+697)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (17/23);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_002947	4,740,820	0	G	T	100.0%	132.9 / NA	41	intergenic (+57/+696)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (17/24);  total (17/24)

AGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCAC  >  NC_002947/4740680‑4740952                                                                                                                                               ||                                                                                                                                     aGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAACGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGc                                                                                                                              <  1:311497/149‑1 (MQ=255) aGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGc                                                                                                                              >  2:94572/1‑148 (MQ=255)     cGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCtt                                                                                                                         <  7:321529/149‑1 (MQ=255)       tACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTcg                                                                                                                       >  3:232103/1‑149 (MQ=255)         cAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTcgcg                                                                                                                     <  2:220560/149‑1 (MQ=255)          aaGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCgg                                                                                                                    <  7:104776/149‑1 (MQ=255)           aGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGc                                                                                                                   <  2:300498/149‑1 (MQ=255)            gATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGcc                                                                                                                  <  1:171619/149‑1 (MQ=255)            gATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCGCTTCGCGGcc                                                                                                                  >  7:376278/1‑149 (MQ=255)              tCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCtt                                                                                                                <  7:126396/149‑1 (MQ=255)                ggCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCgggcaagg                                                                                                              <  6:90254/149‑7 (MQ=255)                ggCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGc                                                                                                              >  5:373637/1‑149 (MQ=255)                   cGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAGAAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGcc                                                                                                             >  1:344558/1‑149 (MQ=255)                       cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGaa                                                                                                       <  5:311485/149‑1 (MQ=255)                          gcCAGCTGAACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag                                                                                                    <  3:52079/149‑1 (MQ=38)                             aGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGcc                                                                                                 <  4:232103/149‑1 (MQ=255)                             aGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGcc                                                                                                 >  5:358758/1‑149 (MQ=255)                                       cGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAC‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAggac                                                                                       <  7:290469/149‑4 (MQ=37)                                                gAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAAc                                                                              >  5:233001/1‑149 (MQ=255)                                                 aaGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCGCTTGGCGGGCTTGCCCGGGAAGAGGCCGGCGCAGCCACCACAAAAcc                                                                             >  6:415226/1‑149 (MQ=255)                                                             gTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCg                                                                                                                                >  5:274404/1‑86 (MQ=255)                                                             gTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCg                                                                                                                                <  6:274404/86‑1 (MQ=255)                                                             ctatctcTGAAAGACCGC‑‑AAGTAAGCTGCATTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCTGCATCTTCTCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTtctc                                                                 <  7:116378/143‑1 (MQ=255)                                                                 cccTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTATTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTccgcc                                                             >  7:298484/1‑149 (MQ=255)                                                                  ccTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCACATCCCGGCCTTGCCCGCGAACAGGCCCGCCCACACCCCCCAAAACCTCAGTATATCTacgccc                                                            >  6:4048/1‑149 (MQ=255)                                                                    tGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTccgc                                                              >  1:257609/1‑145 (MQ=255)                                                                    tGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTccgc                                                              <  2:257609/145‑1 (MQ=255)                                                                    tGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAG‑CATTTTTTATTTGTCCTGTGCCGGCCTCTTAGCGGCCTTGCCAGCGAAGAGGCCGGCACACACACAACAAAACCTAAGTTTTTATccagatct                                                          >  8:116378/1‑143 (MQ=255)                                                                      aacgACCGC‑‑AAGAAAGCTGCAGTAGCCGAACGCAA‑CACGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTCCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACGGACACCACAAAACCTCAGTTTTTCTccgcccgc                                                          <  2:344558/144‑1 (MQ=255)                                                                           cccc‑‑AAGTACGCTCCAGTAGCCCACCGCAC‑GAAGGCGGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGCCCTCTCCGCGGCCTGGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCa                                                   <  5:415226/146‑1 (MQ=255)                                                                           ccGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCa                                                   <  6:358758/149‑1 (MQ=255)                                                                                       gCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCGTGCCCGCGAAGAGGCCGGCCCAGACCCCCCAAAACCACAGTTTTTGTACGCCCGCGCCCGCAGCCCGTTAAg                                         >  6:275809/1‑149 (MQ=255)                                                                                        cgccAGTAGCCGAACGCAA‑GACGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCTAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAgg                                        <  6:233001/146‑1 (MQ=255)                                                                                           ccgTAGCCGACCCCAA‑CAAGGCTGCCCGCGGCCAG‑CTTTTTTATTTTGTCCTGTGCCGCCCGCTGCGCGGCCTGGCCCCCGACGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTa                                     <  4:407382/147‑1 (MQ=255)                                                                                           cAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTa                                     <  6:79001/149‑1 (MQ=255)                                                                                             gaaGCCGAACGAAT‑TATGGCTGCCCTGGGGTAG‑CGTTTTTTATTTGTCCTGTGCCGGCGTCTTCGCGGCCTGGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCTCGCAGCCCTTTCAGGGTAtt                                   <  1:124028/147‑1 (MQ=255)                                                                                                     tcGCAA‑GTAGGCTGCCCGCGGGCAG‑CTTTTTTTTTTTGTCTTGTGGCGGCTGTTTCGCGGCCTTGCGCGGTAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGgcg                           <  5:4048/148‑1 (MQ=255)                                                                                                               ggCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATccacca                  >  3:133438/1‑149 (MQ=255)                                                                                                                  tGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTAGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACg                >  7:359611/1‑148 (MQ=255)                                                                                                                          gggacgcTTTTTTTTTTTGTCCTGGCCCGCCCTCTGCCCGGCCTGGCCCGCTATGTGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACttgtt        <  7:275148/143‑1 (MQ=255)                                                                                                                                ccttttttATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGccac  >  1:76675/3‑149 (MQ=255)                                                                                                                                               ||                                                                                                                                     AGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGC‑‑AAGTAAGCTGCAGTAGCCGAACGCAA‑GAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCAC  >  NC_002947/4740680‑4740952

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: ‑