Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,173,247	G→C	9.4%	intergenic (‑288/+44)	fadD‑I ← / ← fadD‑II	long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,173,247	0	G	C	9.4%	142.9 / 5.7	52	intergenic (‑288/+44)	fadD‑I/fadD‑II	long‑chain‑fatty acid‑‑CoA ligase/long‑chain‑fatty acid‑‑CoA ligase
Reads supporting (aligned to +/- strand):  ref base G (24/22);  new base C (3/2);  total (28/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

GGCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTG  >  NC_002947/5173099‑5173390                                                                                                                                                      |                                                                                                                                                 ggCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTg‑g                                                                                                                                                  <  2:284759/149‑1 (MQ=255)    cAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTg‑gg                                                                                                                                                 >  8:86152/1‑147 (MQ=255)     aaaaCAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAg                                                                                                                                              >  5:172591/1‑149 (MQ=255)              cTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGc                                                                                                                                     <  1:274984/149‑1 (MQ=255)              cTTATGGTCACAAAAATGACTCAATGAACAATACAGCTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTG‑CCCAATGTAGGAGc                                                                                                                                     <  2:43492/149‑1 (MQ=39)               ttATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGATAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCg                                                                                                                                    >  5:132368/1‑149 (MQ=255)                     tCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTTAAACCCCAACTAAATTG‑TGCAGTGTATGACGGGG‑ttt                                                                                                                              >  6:53406/1‑148 (MQ=255)                     tCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTa                                                                                                                             <  6:172591/149‑1 (MQ=255)                     tCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTa                                                                                                                             >  2:178504/1‑149 (MQ=255)                      cacaAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTAc                                                                                                                            >  1:73158/1‑149 (MQ=255)                       acaAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTAcc                                                                                                                           <  2:73158/149‑1 (MQ=255)                                    aaTGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑GTTACCCGCGAAGAAGcc                                                                                                               >  3:180707/1‑148 (MQ=255)                                       gAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATcc                                                                                                           >  2:111920/1‑149 (MQ=255)                                           aaTACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGt                                                                                                       <  7:86152/149‑1 (MQ=255)                                                aGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCAc                                                                                                  >  7:134448/1‑149 (MQ=255)                                                  gTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGc                                                                                                >  6:332906/1‑149 (MQ=255)                                                            gagTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGATAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATcgcg                                                                                       <  6:132368/148‑1 (MQ=255)                                                                     tCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCcgcg                                                                                                                       <  8:81622/107‑1 (MQ=255)                                                                     tCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCcgcg                                                                                                                       >  7:81622/1‑107 (MQ=255)                                                                     tCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgc                                                                             >  7:202496/1‑149 (MQ=255)                                                                        aaaaTGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGAATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgccg                                                                           >  1:133100/1‑148 (MQ=255)                                                                              tggCATATAAGGCTGTATAGAGCGTGTTAGAGCGGTTTACGGCATGCGGGGTTAAACCCGCTCGTACATTG‑GGCCGTGTCGTAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAAt                                                                     <  1:178504/146‑1 (MQ=255)                                                                                gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCtt                                                                  <  8:134448/149‑1 (MQ=255)                                                                                gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCtt                                                                  >  1:266203/1‑149 (MQ=255)                                                                                  aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGGTTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                 <  1:271248/149‑1 (MQ=255)                                                                                  aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGc                                                                <  8:1196/149‑1 (MQ=255)                                                                                  aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGc                                                                <  2:133100/149‑1 (MQ=255)                                                                                        ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGGGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATcgcg                                                                                       <  1:246272/120‑1 (MQ=255)                                                                                        ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATcgcg                                                                                       >  2:246272/1‑120 (MQ=255)                                                                                        ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATc                                                                    <  3:34807/139‑1 (MQ=255)                                                                                        ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATc                                                                    >  4:34807/1‑139 (MQ=255)                                                                                            gTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                 >  7:80310/1‑138 (MQ=255)                                                                                            gTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTg                                                                 <  8:80310/138‑1 (MQ=255)                                                                                                 gagCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGCGTCCGGGATACCCCCAC‑AATACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATg                                                  <  1:111920/149‑1 (MQ=255)                                                                                                      tGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACTGGCGTCATGGGCAAc                                            >  1:217325/1‑149 (MQ=255)                                                                                                             gCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcgc                                     >  3:88731/1‑149 (MQ=255)                                                                                                                 tttAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCgcag                                 >  4:27280/1‑149 (MQ=255)                                                                                                                    aaGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATgg                                                 >  1:264225/1‑130 (MQ=255)                                                                                                                    aaGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATgg                                                 <  2:264225/130‑1 (MQ=255)                                                                                                                     aGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGAATCGCGCAGCAc                              >  5:348811/1‑148 (MQ=255)                                                                                                                             gcgGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCtt                     <  2:266203/149‑1 (MQ=255)                                                                                                                               ggggAAACCCGCTCCTACTTTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                   <  3:83698/149‑1 (MQ=255)                                                                                                                               gggTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                   <  8:202496/149‑1 (MQ=255)                                                                                                                                 gTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTggg                  >  5:280795/1‑148 (MQ=255)                                                                                                                                  tAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTa                >  1:133097/1‑149 (MQ=255)                                                                                                                                   aaaCCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcgcg                                    >  3:67560/1‑128 (MQ=255)                                                                                                                                   aaaCCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcgcg                                    <  4:67560/128‑1 (MQ=255)                                                                                                                                      cacGCTCCTACACTG‑CCCAATGTAGGAGCGGG‑TTTACACGCGAAGATGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt            >  3:120473/3‑149 (MQ=38)                                                                                                                                       ccGCTCCTACACTG‑CCCAATGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTg           >  8:210707/1‑149 (MQ=255)                                                                                                                                         gCTCCTACACTG‑CCCAATGTAGGAGCGGG‑TTTACCCGCGAATAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCAGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTg           >  3:266300/1‑147 (MQ=38)                                                                                                                                             cTACACTG‑CCCAATGTAGGAGCGGG‑TTTACCCGCGAATAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGcc      <  4:266300/148‑1 (MQ=39)                                                                                                                                                cATTG‑GTCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCgg    <  4:88731/147‑1 (MQ=255)                                                                                                                                                cATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTg  <  5:332906/149‑1 (MQ=255)                                                                                                                                                 aTTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGACGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAAACTTGCCCACCCGCGTCATGGGCACCGATTCGCGCAGCACGATGTGCTTGGGTACATTGAAGCCGGtc  >  2:34990/1‑147 (MQ=255)                                                                                                                                                      |                                                                                                                                                 GGCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTG‑GGCAGTGTAGGAGCGGG‑TTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTG  >  NC_002947/5173099‑5173390

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: ‑