Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	BS168_reference_genome	2,003,744	T→C	8.7%	K68R (AAA→AGA)	yoeC ←	putative bacteriophage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	2,003,744	0	T	C	8.7%	128.3 / 4.8	46	K68R (AAA→AGA)	yoeC	putative bacteriophage integrase
Reads supporting (aligned to +/- strand):  ref base T (23/19);  new base C (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.15e-01

CTGTAGGCCTGAATGCGGGAAATCGGCTTCCTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATAAACA  >  BS168_reference_genome/2003615‑2003858                                                                                                                                  |                                                                                                                   cTGTAGGCCTGAATGCGGGAAATCGGCTTCCTGGTCCGCTCTGATTTAAAAAGATATTCGATTTCCTTCATGTCTTTCGAATACTCGTATATTTCCTGTTTCAGCGATTGTAAAAAAAGAATCTTTCTTTTCtttttgg                                                                                                           >  5:112533/1‑137 (MQ=255)    tAGGCCTGAATGCGGGAAATCGGCTTCCTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGtt                                                                                                         <  6:65301/138‑1 (MQ=255)                      aTCGGCTTCCTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCAt                                                                                       >  8:233571/1‑138 (MQ=255)                      aTCGGCTTCCTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCAt                                                                                       >  2:343354/1‑138 (MQ=255)                               cTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCtt                                                                             >  7:421288/1‑139 (MQ=255)                               cTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCtt                                                                             >  2:299664/1‑139 (MQ=255)                                       cACTGATTTAAAAATATATTAGTTTTCCTTCATGTCTTTAGTATACTCGTATATTTCCTGTATCATCGATTCTAAAATAAGAATCTTTCTTTTCTTTATCGTTTTGCTTTCAGTCGCCAATAAATGATCTTTATTTTGa                                                                     <  7:272013/139‑1 (MQ=255)                                        aCTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGaa                                                                    <  7:233571/139‑1 (MQ=255)                                        aCTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGaa                                                                    <  5:322612/139‑1 (MQ=255)                                         cTGATTTAAAAAGATATTCGGTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAAc                                                                   <  3:240528/139‑1 (MQ=255)                                             tttAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTcc                                                               >  5:174068/1‑139 (MQ=255)                                                             ttttCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCa                                               <  7:270822/139‑1 (MQ=255)                                                                tCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGaa                                            >  3:10818/1‑139 (MQ=255)                                                                  cTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGtt                                                                                                         <  8:78290/76‑1 (MQ=255)                                                                  cTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGtt                                                                                                         >  7:78290/1‑76 (MQ=255)                                                                  cTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAat                                           <  8:163214/138‑1 (MQ=255)                                                                  cTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAat                                           <  2:100118/138‑1 (MQ=255)                                                                      aTGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAg                                      <  2:252261/139‑1 (MQ=255)                                                                            ttCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATAc                                >  8:408634/1‑139 (MQ=255)                                                                              cGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACg                               <  2:8597/138‑1 (MQ=255)                                                                                     tCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAgcgcgc                       >  8:72711/1‑139 (MQ=255)                                                                                       gTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTg                     >  6:141908/1‑139 (MQ=255)                                                                                       gTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTg                     >  4:36191/1‑139 (MQ=255)                                                                                       gTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCAGAAATGATCTTTATTTTGAAGGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGAGCGCTg                     >  2:281145/1‑139 (MQ=255)                                                                                       gTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCCTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTCCTGCGTCAGAATATCAGAAATACGGAGCGCGCTg                     >  6:20051/1‑139 (MQ=255)                                                                                          tatTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGtt                   >  4:419426/1‑138 (MQ=255)                                                                                          tatTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGGCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGtt                   <  1:343354/138‑1 (MQ=255)                                                                                          tatTTCCTGTTGCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTg                  <  3:331449/139‑1 (MQ=255)                                                                                          tatTTACTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTTCTATCAGTCGCCCATAAAAGATCTTTATTTTGAACGTCCTTCACTTGCTGCGGCAGAATATCAGAAATACTCAGCGCGCTGtt                   >  2:12940/1‑138 (MQ=255)                                                                                               ccTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGaa                                                                    >  1:251881/1‑84 (MQ=255)                                                                                               ccTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGaa                                                                    <  2:251881/84‑1 (MQ=255)                                                                                               ccTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGcc             >  2:70584/1‑139 (MQ=255)                                                                                               ccTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAAAGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGcc             >  2:102898/1‑139 (MQ=255)                                                                                               ccTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTACTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTAGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGcc             >  3:19290/1‑139 (MQ=255)                                                                                                 tGTTTCAGCGATTTTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCgg                                                 >  5:55672/1‑101 (MQ=255)                                                                                                 tGTTTCAGCGATTTTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCgg                                                 <  6:55672/101‑1 (MQ=255)                                                                                                 tGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCTGAAATACGGAGCGCGCTGTTGATGCCg            >  1:383539/1‑138 (MQ=255)                                                                                                       aGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATa      >  6:366117/1‑138 (MQ=255)                                                                                                       aGCGATTCTAAAATAAGAATCTTTCTTCTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATa      >  2:280977/1‑138 (MQ=255)                                                                                                       aGCGATTCTAAAATAAGAATCTTTCTTCTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATa      >  2:275153/1‑138 (MQ=255)                                                                                                        gCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATaaa    <  5:366117/139‑1 (MQ=255)                                                                                                        gCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATaaa    <  5:286097/139‑1 (MQ=255)                                                                                                        gCGATTCTAAAATAAGAATCTTTCTTCTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATaaa    <  1:280977/139‑1 (MQ=255)                                                                                                        gCGATTCTAAAATAAGAATCTTTCTTCTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATaaa    <  1:275153/139‑1 (MQ=255)                                                                                                          gATTCTAACATAAGACTCTTTCTTTTCTTTTTCGTTGTGCGTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATAAACa  <  5:374725/139‑1 (MQ=255)                                                                                                          gATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATAAACa  <  7:29821/139‑1 (MQ=255)                                                                                                                                  |                                                                                                                   CTGTAGGCCTGAATGCGGGAAATCGGCTTCCTGGTCCGCACTGATTTAAAAAGATATTCGTTTTCCTTCATGTCTTTCGTATACTCGTATATTTCCTGTTTCAGCGATTCTAAAATAAGAATCTTTCTTTTCTTTTTCGTTTTGCTTTCAGTCGCCCATAAATGATCTTTATTTTGAACGTCCTTCACTTGCAGCGGCAGAATATCAGAAATACGGAGCGCGCTGTTGATGCCGAAAATAAACA  >  BS168_reference_genome/2003615‑2003858

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: ‑