Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,729,405	C→G	8.6%	intergenic (‑34/+38)	xylB ← / ← xylA	xylulokinase/xylose isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,729,405	0	C	G	8.6%	163.6 / 9.0	58	intergenic (‑34/+38)	xylB/xylA	xylulokinase/xylose isomerase
Reads supporting (aligned to +/- strand):  ref base C (24/29);  new base G (3/2);  total (27/31)
Fisher's exact test for biased strand distribution p-value = 6.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.48e-02

GGCGCGAAACGGTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGAGCATATTTGGCTAAATC  >  NC_000913/3729266‑3729547                                                                                                                                             |                                                                                                                                               ggCGCGAAACGGTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTAc                                                                                                                                             <  1:670572/143‑1 (MQ=255) ggCGCGAAACGGTCAGCTCTTCCGTTTGCGCAGCAACAACATCACCCTGCTCGTTGAGCAAAATAACTTCCACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTAc                                                                                                                                             <  1:519831/143‑1 (MQ=255)          cGGTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGGTTATCGGTAGCGATaccg                                                                                                                                     <  2:252772/143‑4 (MQ=255)          cGGTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCg                                                                                                                                    <  1:672568/143‑1 (MQ=255)           ggTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGGTTATCGGTAGCGATaccgg                                                                                                                                    <  2:103900/143‑5 (MQ=255)            gTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTCGCTTAAAAAAAGACCCTG‑TACCGCTACCGAttcacggc                                                                                                                                  >  1:370364/1‑136 (MQ=255)             tCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCGCGAGGTGCCTAGATCTATCCCGATATACATATCGATCGTTCACTAAAAAAATGCACGG‑CATCGCTACCGATAACCAGGc                                                                                                                                 >  2:297542/1‑143 (MQ=255)                  ttttCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACg                                                                                                                            <  1:497902/143‑1 (MQ=255)                      ccGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGCTCACTAAAAAAAAGCAGGG‑TGTCGCTACCGATAACCGGGCCAACGGACt                                                                                                                        >  1:884708/1‑143 (MQ=255)                        gTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACAGATAACCGGGACACCGGACTGc                                                                                                                      >  2:169316/1‑143 (MQ=255)                         tttGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGca                                                                                                                     >  2:875934/1‑143 (MQ=255)                                agcaACCACCTCACCCTGCTCGTCGAGCAAAATCACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAg                                                                                                              <  1:212272/143‑1 (MQ=255)                                    accaccTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGt                                                                                                          >  2:80873/1‑143 (MQ=255)                                     ccaccTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCCCCGTTAGCCGtt                                                                                                         >  2:368951/1‑143 (MQ=255)                                         accACCCCGCTCGTTGAGCAAAATCACCTTTACGCCCGAGGTGCCAAGCTCTATCCCGATATCCTTATCGATCGTTCCTGAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTAttt                                                                                                     <  1:253202/141‑1 (MQ=255)                                           cACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCACGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGt                                                                                                   >  2:636295/1‑143 (MQ=255)                                           cACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGt                                                                                                   <  2:736793/143‑1 (MQ=255)                                           cACCCTGCTCGCTGAGCAAACTAACTTTTACGCCCGAGGTGCCAAGATCCATCCCGATATACATATCGATCGTTCCTTAACAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGt                                                                                                   <  1:289423/143‑1 (MQ=255)                                              ccTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATGTGTCGa                                                                                                >  1:839918/1‑143 (MQ=255)                                                tGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑GATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGatc                                                                                              <  2:232122/143‑3 (MQ=255)                                                 gCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACCGCACAGTTAGAACTTATTTGTCGAACa                                                                                             >  2:530259/1‑143 (MQ=255)                                                   tCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGa                                                                                           <  1:486233/143‑1 (MQ=255)                                                     gTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATa                                                                                         >  2:461593/1‑143 (MQ=255)                                                        gAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTAGCCCGATACACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATg                                                                                      <  1:250649/143‑1 (MQ=255)                                                           cAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGAGAAAGGtt                                                                                   >  2:420233/1‑143 (MQ=255)                                                                  aCTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGa                                                                            <  1:89938/143‑1 (MQ=255)                                                                   cTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAgct                                                                           >  1:835938/1‑141 (MQ=255)                                                                    ttttACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACGGCACAGTTAGCCGTTATTTGTCGCACAGATAATGGGTTACACGAtt                                                                          >  1:278080/1‑143 (MQ=255)                                                                         cGCCCGCGGTGCCAAGATCTGTCCCGATCTACATATCGATCGTTCCTTCAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCa                                                                     <  2:373237/143‑1 (MQ=255)                                                                         cGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCa                                                                     <  1:580915/143‑1 (MQ=255)                                                                                   tccAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTg                                                           <  1:670450/142‑1 (MQ=255)                                                                                     cAAGATCTATCACGATATACATATCAATCGTTCCTTAAAAAAATGCGCGG‑TATCACTACCGAAAACCGGGCCAACGGAATGCACAGTTAGCCGGTAATTGTCGAACAGATAATGGTTGACCAGATTTATCAGTTGGTCATGGc                                                         >  2:807437/1‑143 (MQ=255)                                                                                     cAAGATCTAGCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGc                                                         <  1:828968/143‑1 (MQ=255)                                                                                        gaccTATCCCGATATACATATCGATCCTCCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGAc                                                      <  1:29657/140‑1 (MQ=255)                                                                                         accTATCCCGATATACATATCGATCGTTCCTTAAAAAAATTCCCGG‑TATCGCTACTGATAACCGGGTCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGAcc                                                     <  2:596734/141‑1 (MQ=255)                                                                                             aTCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTCTTTATAGAAAAAAAAATGGTTTAACAGATTTTCCAGTTGTTCCTGGCGACCActc                                                 >  1:78428/1‑143 (MQ=255)                                                                                              tCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCActct                                                <  1:530259/143‑1 (MQ=255)                                                                                               cccGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTg                                               <  1:80873/143‑1 (MQ=255)                                                                                               cccGATAGACGTATCGATCGTGCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTg                                               <  1:688106/143‑1 (MQ=255)                                                                                                 cGATATACATATCGATCGTTCCTTCAAAAAATGCCCGT‑TATCGCTACCGAGAACCGCGCCAACGCACGGCACACTTAGCCCTTATTTGCCGCACACACATTGCTCTCCCACATCTTCCAGTTCCTCCTGGCGACCACTCTGag                                             >  2:144852/1‑142 (MQ=255)                                                                                                 cGATATACATATCGAGCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGAt                                             <  1:274594/143‑1 (MQ=255)                                                                                                        cATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGACCAGCTACTGGTTTCCCAGATTCTCCCGTCTTTCCTCACGCCCCCTCTGATGCGCCgg                                      >  2:689735/1‑143 (MQ=255)                                                                                                         atatCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACAGACTGCACAGTTAGCCGTTATTTCTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGTCGAACCCTCTGACCCAccagc                                     >  2:230501/1‑140 (MQ=255)                                                                                                           atcgatcgTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGACTTTCCAGTTGTTACTGGCGACAACACTTCTGCACCGtaga                                   >  2:296942/1‑143 (MQ=255)                                                                                                                tcgTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAat                              <  2:248616/143‑1 (MQ=255)                                                                                                                   ttCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGCGACAAatgat                           >  2:267528/1‑143 (MQ=255)                                                                                                                       ttAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTc                       >  1:738057/1‑143 (MQ=255)                                                                                                                       ttAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTc                       >  1:536054/1‑143 (MQ=255)                                                                                                                           aaaaaTGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGACGTGTTTATGCGGACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGa                   <  1:651291/143‑1 (MQ=255)                                                                                                                           aaaaaTGCCCGG‑TATCGCGACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGa                   <  2:471756/143‑1 (MQ=255)                                                                                                                                   ccggttATCGGTAGCGAT‑ACCGGGCCAACGGACTGCACAGTTCGCCGTTATTTGTCGAACCGATAATGGTTTACCCGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGCGCACAttt           >  2:175582/6‑143 (MQ=255)                                                                                                                                   ccggttATCGGTAGCGAT‑ACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGGCCACTCTGATGCACTGGAGACCAATGATGTTCCTGAGCATAttt           >  2:881545/6‑143 (MQ=255)                                                                                                                                   ccggttATCGGTAGCGAT‑ACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATAATGTTCGTGAGCATAttt           >  1:288712/6‑143 (MQ=255)                                                                                                                                   ccGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGTTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACTGGAGACAAATGATGTTCCTGAGCATAttt           <  1:61825/143‑1 (MQ=255)                                                                                                                                   ccGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGAGCATAttt           <  1:875934/143‑1 (MQ=255)                                                                                                                                    cGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGAGCATATTTg          <  1:142089/143‑1 (MQ=255)                                                                                                                                     gg‑TATCGCTACCGATAACCAGGCCAACGGACTGCACAGTTAGCCGGAATTTGTCGAACAGAGAATGGTTTACCAGATTTTCCACTTGTTCCTGGCGACCACTCAGATGCACCGGAAACAAATGGAGTTCCCGAGAACAtttcg         >  2:323937/1‑141 (MQ=255)                                                                                                                                            gCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGAGCATATTTGGCTAAAt   <  2:411915/143‑1 (MQ=255)                                                                                                                                             cTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCCGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGCCAAATGATGTTCCTGAGCATATTTGGCTAACTc  >  1:822967/1‑143 (MQ=255)                                                                                                                                             |                                                                                                                                               GGCGCGAAACGGTCAGCTTTTCCGTTTGCGCAGCAACCACCTCACCCTGCTCGTTGAGCAAAATAACTTTTACGCCCGAGGTGCCAAGATCTATCCCGATATACATATCGATCGTTCCTTAAAAAAATGCCCGG‑TATCGCTACCGATAACCGGGCCAACGGACTGCACAGTTAGCCGTTATTTGTCGAACAGATAATGGTTTACCAGATTTTCCAGTTGTTCCTGGCGACCACTCTGATGCACCGGAGACAAATGATGTTCCTGAGCATATTTGGCTAAATC  >  NC_000913/3729266‑3729547

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑