Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,740,841	0	T	A	28.8%	66.4 / 31.3	52	intergenic (+78/+675)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base T (17/20);  new base A (5/10);  total (22/30)
Fisher's exact test for biased strand distribution p-value = 5.39e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.25e-02
Rejected as consensus: Frequency below/above cutoff threshold.

TCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCA  >  NC_002947/4740693‑4740987                                                                                                                                                     |                                                                                                                                                   tCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCtt                                                                                                                                                   <  4:341224/149‑1 (MQ=255)   ggCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTg                                                                                                                                                  <  5:36797/148‑1 (MQ=255)   ggCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTg                                                                                                                                                  <  3:11458/148‑1 (MQ=255)          cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGaa                                                                                                                                          <  1:183102/149‑1 (MQ=255)          cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGaa                                                                                                                                          <  5:279451/149‑1 (MQ=255)          cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGaa                                                                                                                                          <  2:228337/149‑1 (MQ=255)           gcgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGaa                                                                                                                                          >  8:15682/1‑148 (MQ=255)            cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGTAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAaga                                                                                                                                        <  5:387835/149‑1 (MQ=38)            cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAaga                                                                                                                                        <  7:275257/149‑1 (MQ=38)             gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag                                                                                                                                       <  7:104606/149‑1 (MQ=38)             gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag                                                                                                                                       <  5:99732/149‑1 (MQ=38)                  cTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAAGAGGCCgg                                                                                                                                  <  5:127692/149‑1 (MQ=38)                       cacCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGca                                                                                                                                >  7:336949/1‑146 (MQ=255)                        acCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAgg                                                                                                                            <  7:293730/149‑2 (MQ=37)                         ccGGCGCGCTCAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTCCAGTAGCCGAACCAAAGATGCCTGCCCTCGGGCAG‑CGTTTTTTATTTGTCCTTTGCCGGCGTCTGCGCGGCCTTGCCCGCGAAGTGGCCGGCACAGac                                                                                                                           <  6:385549/149‑1 (MQ=255)                         ccGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGac                                                                                                                           <  7:173126/149‑1 (MQ=255)                         ccGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGac                                                                                                                           >  5:295249/1‑149 (MQ=255)                          cGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGaca                                                                                                                          >  3:221425/1‑149 (MQ=255)                                    aaGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCcgcg                                                                                                                                            <  3:80938/121‑1 (MQ=255)                                    aaGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCcgcg                                                                                                                                            >  4:80938/1‑121 (MQ=255)                                       cgcgACAGCGTTCCCCTTAAAGACCGCAAGTACGCTGCAGTAGCCGACCGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCa                                                                                                             <  5:316627/149‑1 (MQ=255)                                             aTCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGttttt                                                                                                       <  6:295249/149‑1 (MQ=255)                                                     ccTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCATCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCGCAGTGATTCAccgccc                                                                                               >  4:278510/1‑149 (MQ=255)                                                      cTGAAAGACCGCAAGTAAGCTGAAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTATTAGCGGGCTTTCCCGCGAAGAGGCCGGGACCGGCACCCCAAAACCACAGGTTTTGTccgcccg                                                                                              >  7:246448/1‑149 (MQ=255)                                                       tGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCATCGCGGCCTTGCCCCCGAAGAGGCCGGCACAGACACCACAAAACCTCACGTTTTATccgcccg                                                                                              >  1:375378/1‑148 (MQ=255)                                                         aaaGACCTCAAGTAAGCTCCAGTCGCCGAACCCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGGGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCt                                                                                            <  3:94332/148‑1 (MQ=255)                                                         aaaGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTccgcccgc                                                                                             <  3:46018/147‑1 (MQ=255)                                                          aaGACCGCAAGTACGCTTCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGAAGCC‑TTTTTTATTTTTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTc                                                                                           <  7:250701/148‑1 (MQ=255)                                                           aGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTATTTCTCCGCCCGCTCAc                                                                                         >  5:99026/1‑149 (MQ=255)                                                                  aaGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGccc                                                                                  <  6:191105/149‑1 (MQ=255)                                                                         cTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGttttt                                                                                                       >  2:320675/1‑121 (MQ=39)                                                                         cTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGttttt                                                                                                       <  1:320675/121‑1 (MQ=39)                                                                            cAGTACCCGAACCCAAGATGGCTGCCGTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGCGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAggg                                                                          <  3:278510/147‑1 (MQ=255)                                                                                  ccGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTATTAGCCGCCATGCCCGCGCAGAGGCCCGCACAGCCACCCCAAAAACACAGATTTTATACGCCCCCTCACCCCGCCCTATCAGGGGATTTaa                                                                   >  8:155705/1‑148 (MQ=255)                                                                                    gAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag                                                                                                                                       <  3:187936/78‑1 (MQ=17)                                                                                    gAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGGCAAGGCCGCGAagag                                                                                                                                       >  4:187936/1‑78 (MQ=17)                                                                                               ggCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATccacca                                                     >  6:76510/1‑149 (MQ=255)                                                                                                    cccTGGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAATGGCGCATCCACCACGAAc                                                <  5:166249/149‑1 (MQ=255)                                                                                                           ggaagcattttttATTGGTCCTGGGCCGGCCGCTTCGCGGCCTTGCCCGCTACTAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACttgttg                                          <  7:15682/142‑1 (MQ=255)                                                                                                           gCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGCGGCTTTGCCCGCTAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTgg                                         <  7:155705/149‑1 (MQ=255)                                                                                                                ccttttttATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCGCAGTTTTTATCCGCCCGCACACCCAGCCCATTCAAGGTATTGAAAGGCGCAACCACCAAGAACATGTTTGccac                                     >  2:322745/3‑149 (MQ=255)                                                                                                                       tATTTGTCCTGTGCCGGCCTCTTCGCGGCCTTGCCCGCTAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGc                               <  1:322745/148‑1 (MQ=255)                                                                                                                            gtcctgTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCAc                         >  2:66683/6‑149 (MQ=255)                                                                                                                               ctgcgCCGGCCTCTTCGCGGCCTTGCCCGCGATGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGc                       <  3:219207/144‑1 (MQ=255)                                                                                                                               ctgTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTGTTTCTCCGCCAGCTCACGCCGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGACGGCACGc                       >  7:354102/3‑148 (MQ=255)                                                                                                                                       gCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCCCGCTACCACCTg              >  8:261272/1‑149 (MQ=255)                                                                                                                                          tctTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCt           >  3:89560/1‑149 (MQ=255)                                                                                                                                          tctTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCt           >  1:297682/1‑149 (MQ=255)                                                                                                                                           ctTCGCGGGCAAGGCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTc          >  8:176813/1‑149 (MQ=255)                                                                                                                                              cgcgGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGc                           <  4:169029/129‑1 (MQ=255)                                                                                                                                              cgcgGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGc                           >  3:169029/1‑129 (MQ=255)                                                                                                                                                cgGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGgtgt     <  4:221425/149‑1 (MQ=255)                                                                                                                                                   ccTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCa  >  6:234134/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                   TCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGCGGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTATTGAACGGCGCATCCACCACGAACTTGTTGGCCACCATCGCCGGCACGCTACCACCTGGCTCGGTGTGCA  >  NC_002947/4740693‑4740987

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: ‑