Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,173,247	G→C	18.7%	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	18.7%	89.1 / 17.9	43	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 (20/14);  new base C (3/5);  total (24/19)
Fisher's exact test for biased strand distribution p-value = 4.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.56e-01

GCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGTT  >  NC_002947/5173100‑5173395                                                                                                                                                    |                                                                                                                                                     gCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTggg                                                                                                                                                     >  2:213165/1‑149 (MQ=255)      aaCAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAgtg                                                                                                                                                <  4:159188/149‑1 (MQ=255)                aTGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGTGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                                       <  4:3071/148‑1 (MQ=255)                aTGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCgg                                                                                                                                       <  8:38263/148‑1 (MQ=255)                aTGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCgg                                                                                                                                       <  7:6750/148‑1 (MQ=255)                 tGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCggg                                                                                                                                      <  3:213873/148‑1 (MQ=255)                  ggTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCggg                                                                                                                                      <  8:219005/147‑1 (MQ=255)                  ggTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCggg                                                                                                                                      >  7:219005/1‑147 (MQ=255)                       caAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTAccc                                                                                                                               <  1:213165/149‑1 (MQ=255)                                cTCAATGAAAAATACAGGTCATTTTTATATTAATTATCAAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCgaatgcc                                                                                                                      <  6:260986/149‑5 (MQ=25)                                 tCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGc                                                                                                                     >  3:40922/1‑149 (MQ=255)                                     tcaaaaaTACTGTTCATTTTTATATTAATTATCAAAAATGTCGCATATACGGCTTTATATCGCCTGTTAGAGCGTTTTATGCCATTCGCGGGTAACCCCGCTCCTACATTGGGCAGTGTTGTTGGGGTTTTACCCGCGAAGAAGCCATc                                                                                                                 <  4:152318/144‑1 (MQ=255)                                            tACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTa                                                                                                           >  7:255967/1‑148 (MQ=255)                                                 gTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCCCGAAGAAGCCATGCCGGTATCACg                                                                                                      >  3:130685/1‑148 (MQ=255)                                                              tAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCCCGCTATATCGCGCAAc                                                                                        >  4:166894/1‑149 (MQ=255)                                                                    tCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCccgc                                                                                  >  4:86649/1‑149 (MQ=255)                                                                       aaaaTGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGTGCAGTGTAGGAGAGGGTTTACCCGCGAAGAAGCAATACAGGTATAACGCTATATAGCGCAACTAccgccg                                                                                >  3:17623/1‑148 (MQ=38)                                                                                 aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGc                                                                                                                     >  6:89070/1‑101 (MQ=255)                                                                                 aGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGc                                                                                                                     <  5:89070/101‑1 (MQ=255)                                                                                   aTAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGcc                                                                    >  5:68884/1‑148 (MQ=255)                                                                                       ggCTGTATAGAGCCTGTTAGCGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCg                                                               >  5:115309/1‑149 (MQ=255)                                                                                       ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCg                                                               <  3:86649/149‑1 (MQ=255)                                                                                       ggCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCCCGGCTAAATTGGGCAGTGTAGGGGCGGGTTTACCCGCGAAGAAGCGATCCCGGGATCACGCTATATCGCGGGACTACCGCCGCTAAAAGTTGCCCAcgg                                                               >  4:8869/1‑147 (MQ=255)                                                                                          tGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCg                                                            >  3:71533/1‑149 (MQ=255)                                                                                                 ccccTGTAAGCCCGGTTTAAGGCATTCCCGGGAAAACCCGCTCCTACATTGGCCCGTGTAGGAGCGGGTTAACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATggg                                                     <  8:255967/147‑1 (MQ=255)                                                                                                    cTGTTCGAGCGGTTTATGGCATTCGGGGTTAAACCCGCTCCTACTTTGGGCAGTGTAGGATCGGTTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCaa                                                  <  4:17623/149‑1 (MQ=255)                                                                                                     tGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCACCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGGAAAATCTTGCCCACCGGCGTCATGGGCaa                                                  >  1:272504/1‑148 (MQ=255)                                                                                                            gCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcgc                                          <  6:115309/149‑1 (MQ=255)                                                                                                                    aGGCATTCGCGGGTAAACCCGCACCTACAATGGGCATTGTAGGAGCGGGGTTACCCCCGAATAAGCCATCCCGGTATACCGCTATAAAGCGCAACTACCGCCCCAAAATAATTCCCCACGGCGTCAAGGGCAACACTTCGCccacacc                                   >  6:22539/1‑144 (MQ=255)                                                                                                                    aGGCATTCCCGGGTAAACCCCCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCAc                                   >  6:221449/1‑148 (MQ=255)                                                                                                                     ggCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCTGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGa                                 >  5:125449/1‑149 (MQ=255)                                                                                                                      gCATTCGCGGGTAAACCCGCTCCTACATTTGGCAGTGTAGGAGCGGGTTTAACCGCGAAGAAACCATCCCGGTATAACGCTATATAGCGCAACTCCCGCCGCAAAATCTTTACCACCCGCGGCATGGGCAACGAATCGCGCAGCACGaa                                >  4:16570/1‑148 (MQ=38)                                                                                                                            gcgGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCtt                          >  6:58776/1‑149 (MQ=255)                                                                                                                                     cccGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCACCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcg                                           >  3:211747/1‑123 (MQ=255)                                                                                                                                     cccGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCACCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTcg                                           <  4:211747/123‑1 (MQ=255)                                                                                                                                      ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTg                         >  3:180512/1‑140 (MQ=255)                                                                                                                                      ccGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTg                         <  4:180512/140‑1 (MQ=255)                                                                                                                                      acGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTACAGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTg                >  7:199890/2‑149 (MQ=255)                                                                                                                                       cGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt                 >  3:59033/1‑147 (MQ=255)                                                                                                                                       cGCTCCTACACTGCCCAATGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACttt                 <  4:59033/147‑1 (MQ=255)                                                                                                                                        gCTCCTACACTGCCCAATGTAAGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                        <  7:279529/139‑1 (MQ=39)                                                                                                                                        gCTCCTACACTGCCCAATGTAAGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTgg                        >  8:279529/1‑139 (MQ=39)                                                                                                                                              aCATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGt        >  2:64834/1‑149 (MQ=255)                                                                                                                                               cATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCgg         <  6:68884/147‑1 (MQ=255)                                                                                                                                                    ggCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGtt  >  5:127050/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GCCAAAACAGGCCTTATGGTCACAAAAATGACTCAATGAACAATACAGGTCATTTTTAGAGTAATTATCCAAAATGTCGCAGATAAGGCTGTATAGAGCCTGTTAGAGCGGTTTAAGGCATTCGCGGGTAAACCCGCTCCTACATTGGGCAGTGTAGGAGCGGGTTTACCCGCGAAGAAGCCATCCCGGTATCACGCTATATCGCGCAACTCCCGCCGCAAAATCTTGCCCACCGGCGTCATGGGCAACGATTCGCGCAGCACGATGTGCTTGGGTACTTTGTAGCCGGTGAAGTT  >  NC_002947/5173100‑5173395

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: ‑