Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,740,842	T→A	17.5%	intergenic (+79/+674)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,740,842	0	T	A	17.5%	77.4 / 12.5	40	intergenic (+79/+674)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (21/12);  new base A (4/3);  total (25/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.46e-01

CCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCAC  >  NC_002947/4740697‑4740988                                                                                                                                                  |                                                                                                                                                    ccGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGccc                                                                                                                                                 >  4:72772/1‑149 (MQ=255)       gcgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCcgcg                                                                                                                                              >  2:230392/1‑146 (MQ=255)        cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAaga                                                                                                                                          <  3:44795/149‑1 (MQ=38)              cTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGGCCGCGAAgcgggcgg                                                                                                                                    >  5:29303/1‑149 (MQ=255)                 tACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGca                                                                                                                                  >  3:118526/1‑148 (MQ=255)                  acacCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAAGAggagattcg                                                                                                                                 >  1:47775/1‑141 (MQ=37)                  acacCGGCGAGCAGAAGCGCGACATCGTTGCCCAGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAag                                                                                                                                           >  4:122067/1‑138 (MQ=38)                  acacCGGCGAGCAGAAGCGCGACATCGTTGCCCAGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAag                                                                                                                                           <  3:122067/138‑1 (MQ=38)                          gAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GAcaccac                                                                                                                       <  1:230392/149‑1 (MQ=255)                                aaGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAaga                                                                                                                                          >  8:68508/1‑125 (MQ=255)                                aaGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAaga                                                                                                                                          <  7:68508/125‑1 (MQ=255)                                    gcgACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAg                                                                                                             <  3:72772/149‑1 (MQ=255)                                               gCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTAGCGGCCGTGGCCGCGAAGAGGCCCGGCCA‑GACACCACAAAACCTCAGTTTTtttcaa                                                                                                   >  3:301654/1‑146 (MQ=255)                                                  cTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGt                                                                                                            <  7:193331/136‑1 (MQ=39)                                                  cTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCATCGCGGCCTTGCCCGCGAAGAGGCCCGCCCC‑GACACCACAAAACcacact                                                                                                            >  8:193331/1‑134 (MQ=255)                                                     aaaGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCCCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTATccgcccgca                                                                                             >  7:333023/1‑147 (MQ=255)                                                          ccGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCa                                                                                       >  4:292646/1‑149 (MQ=255)                                                             cAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGACCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGcc                                                                                    >  5:92710/1‑149 (MQ=255)                                                                        cAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTa                                                                         <  3:292646/149‑1 (MQ=255)                                                                        cAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGACCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTa                                                                         <  6:92710/149‑1 (MQ=255)                                                                              ccGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGGTTTTATCCGCCCGCGCACGCCGCCCTTTCAgg                                                                            >  3:60040/1‑140 (MQ=255)                                                                                      aagaagGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTATTCGCGGCCTTGCCCCCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTATCCGCCCCCGAACGCCGCCCATTAAGGGTATTTAACGGCGCaaa                                                           >  4:207527/1‑147 (MQ=255)                                                                                        gaagGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGt                                                                          >  7:110496/1‑132 (MQ=39)                                                                                        gaagGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGt                                                                          <  8:110496/132‑1 (MQ=39)                                                                                            gCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCcaccac                                                     <  4:118526/149‑1 (MQ=255)                                                                                                     gggCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACttgtt                                            <  3:207527/149‑1 (MQ=255)                                                                                                     gggCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACttgtt                                            <  6:332953/149‑1 (MQ=255)                                                                                                     gggCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACttgtt                                            >  1:245020/1‑149 (MQ=255)                                                                                                               tttttATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCAt                                   >  6:146997/1‑149 (MQ=255)                                                                                                                   tATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGc                                <  2:245020/148‑1 (MQ=255)                                                                                                                             gTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTac                     >  2:88702/1‑149 (MQ=255)                                                                                                                                   gCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTg               >  4:147336/1‑149 (MQ=255)                                                                                                                                      tctTCGCGGGCAAGGCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACAACCTGGCt            >  2:262279/1‑149 (MQ=255)                                                                                                                                      tctTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCt            >  2:203156/1‑149 (MQ=255)                                                                                                                                      tctTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCACCGGCACGCTACCACCTGGCt            >  3:126986/1‑149 (MQ=255)                                                                                                                                        ttCGCGGGCAAGGCCGCGAAGAGGCCGGCACAGGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATc                                  <  4:266809/126‑1 (MQ=39)                                                                                                                                        ttCGCGGGCAAGGCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCg          >  8:107606/1‑149 (MQ=255)                                                                                                                                           gcgGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGgtg       >  2:207235/1‑149 (MQ=255)                                                                                                                                           gcgGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGgt        <  1:88702/148‑1 (MQ=255)                                                                                                                                                cTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAGAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCAc  >  1:43691/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACA‑GACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCAC  >  NC_002947/4740697‑4740988

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: ‑