Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,173,247	G→C	18.5%	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	18.5%	106.4 / 21.8	54	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 (20/22);  new base C (4/6);  total (25/29)
Fisher's exact test for biased strand distribution p-value = 7.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.92e-01

CAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTT  >  NC_002947/5173102‑5173380                                                                                                                                                  |                                                                                                                                      cAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCa                                                                                                                                    >  6:1616/1‑149 (MQ=255)  aaaaCAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGACTGTTAGAGCGGTTTAAGGAATTCGCGGGTAAACCCGCTCCTACATTGGGCAg                                                                                                                                   >  7:246975/1‑149 (MQ=255)   aaaCAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGACTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAgt                                                                                                                                  <  1:265813/149‑1 (MQ=255)         gCCTTATGGTAACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGa                                                                                                                            <  4:122360/149‑1 (MQ=39)               tGGTCACAAAAATGACTCAATGAACAATATAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCggg                                                                                                                       <  7:172993/148‑1 (MQ=255)               tGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTTTCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAAACCGCTCCAAAATTTTGCACTGTAGGAGCgggg                                                                                                                      >  2:330773/1‑148 (MQ=255)               tGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGt                                                                                                                      <  5:1616/149‑1 (MQ=255)                 gTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAgtgt                                                                                                                                >  8:253618/1‑137 (MQ=255)                 gTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAgtgt                                                                                                                                <  7:253618/137‑1 (MQ=255)                 gTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                        >  2:5597/1‑145 (MQ=255)                 gTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                        <  1:5597/145‑1 (MQ=255)                   cacaAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                        <  2:94217/143‑1 (MQ=255)                   cacaAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                        >  1:94217/1‑143 (MQ=255)                    acaAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCGGGTTTAc                                                                                                                  <  2:121261/148‑1 (MQ=255)                     caAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTAccc                                                                                                                <  4:279222/149‑1 (MQ=255)                      aaaaaTGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAg                                                                                                                              >  4:220699/1‑134 (MQ=255)                      aaaaaTGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAg                                                                                                                              <  3:220699/134‑1 (MQ=255)                                 aaTGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAATAAGCCa                                                                                                    >  3:297936/1‑149 (MQ=255)                                  aTGAACAATACTGGTCATTTTTATAGTAATTATCAAAATTGCCGCATATAAGGCTGTATAGAGCCTTTAAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGTTTTACCCGCGAAGAAGCCAt                                                                                                   <  6:217887/149‑1 (MQ=38)                                     aaCAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATccc                                                                                                >  1:312120/1‑149 (MQ=255)                                        aaTACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCgg                                                                                              >  6:71892/1‑148 (MQ=255)                                          tACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTAc                                                                                                                  <  7:192876/126‑1 (MQ=255)                                          tACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTAc                                                                                                                  >  8:192876/1‑126 (MQ=255)                                                      ttAGAGTAATTATCCAAAATGTCTCAGATAATGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCTGTATCACGCTATATc                                                                                <  8:246975/148‑1 (MQ=255)                                                                     aaaaTGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgccg                                                                 >  1:218339/1‑148 (MQ=255)                                                                     aaaaTGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgccg                                                                 >  1:240179/1‑148 (MQ=255)                                                                             gCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCtt                                                        <  5:71892/149‑1 (MQ=255)                                                                               aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGc                                                      <  2:49886/149‑1 (MQ=255)                                                                                   aaGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCAc                                                  >  5:75348/1‑149 (MQ=255)                                                                                        tttataGTGCCTGTTAGAGGGTTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCTGTGTAGTTGGGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATcgc                                                                              <  6:20015/114‑1 (MQ=37)                                                                                        tGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATagc                                                                              >  5:20015/1‑116 (MQ=255)                                                                                            taGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTACTACATTGGGGAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCCTACCGGTATAACGCGATATCGAGCAACTCCCGCCGCAAAATCTTGCCCACCGCCGTCAt                                         >  3:210830/1‑149 (MQ=38)                                                                                              gagCCTGTTAGCGCGGTTTAAGGCTTTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGTTTTACCCGCGAAGAAGCCTTCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCATAATCTTGCCCACCGGCGTCATg                                        <  4:210830/148‑1 (MQ=39)                                                                                              gagCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATg                                        <  2:114010/148‑1 (MQ=255)                                                                                              gagCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCAACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATAACGCGCAACGCCCCCCCCAAAAGCTTGCCCCCCGGCGTCAggg                                       >  4:234318/1‑149 (MQ=38)                                                                                                        gagCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTc                             <  2:312120/149‑1 (MQ=255)                                                                                                         agCGGTTTACGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAAc                                  <  5:199469/143‑1 (MQ=255)                                                                                                         agCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGGTTAGGAGCGGGTTTACCCGCGAAGAAGCCATACCGGGATCACCCTATATAGCGCAACAACCGCCGCAAAATAATGCCCACCGGCGGCAAGGGCacccatc                              >  6:199469/1‑141 (MQ=25)                                                                                                          gCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCaa                                                                          >  1:135065/1‑102 (MQ=255)                                                                                                          gCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCaa                                                                          <  2:135065/102‑1 (MQ=255)                                                                                                          gCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcgc                           <  2:240179/149‑1 (MQ=255)                                                                                                                      cttCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGAtgt               >  1:268589/2‑149 (MQ=255)                                                                                                                        tCGCGGGTAAAACCCCTCCGAAAATGGTCAGTGTAGGAGCGGGTTTAAACGCGAATAAGGAATACCAGTATCACTCAAATAAGCGCAACACCCACCCCAAAATATTGCCCAACGGAGTCAAGGCAAACGATTCCGGCAGCACCAagtg              >  8:189787/1‑148 (MQ=255)                                                                                                                          gcgGGCAACCCCGTTCCTACATGGTGCAGGGACTCAGCGGGTTAACCCTCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGCGCAACTATTCGCGCAGCACGATGTGCtt           <  8:113203/149‑1 (MQ=255)                                                                                                                            gtgTAAACCCGCTCAAAATTGGGGCAGTCTCGGAGCGGTTTAACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg         <  1:330773/147‑1 (MQ=255)                                                                                                                            gggTAAACCCGCTCCTACCCTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg         <  2:268589/149‑1 (MQ=38)                                                                                                                             ggTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTggg        <  2:218339/149‑1 (MQ=255)                                                                                                                                  aCCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACtt   >  2:114631/1‑149 (MQ=255)                                                                                                                                  aCCCGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACtt   >  3:189660/1‑149 (MQ=255)                                                                                                                                   cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTg          <  7:108535/141‑1 (MQ=255)                                                                                                                                   cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTg          >  8:108535/1‑141 (MQ=255)                                                                                                                                   cccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt  <  4:189660/149‑1 (MQ=255)                                                                                                                                    ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTc                             <  2:349585/121‑1 (MQ=255)                                                                                                                                    ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTc                             >  1:349585/1‑121 (MQ=255)                                                                                                                                                 gggCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg         >  5:321335/1‑128 (MQ=255)                                                                                                                                                 gggCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg         <  6:321335/128‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                      CAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTT  >  NC_002947/5173102‑5173380

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: ‑