Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	391,703	(G)6→7	pseudogene (1453/1458 nt)	yaiT →	putative autotransporter YaiT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	391,697	1	.	G	87.8%	121.7 / 10.3	41	pseudogene (1447/1458 nt)	yaiT	putative autotransporter YaiT
Reads supporting (aligned to +/- strand):  ref base . (3/2);  new base G (18/18);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACTTCAGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑T‑G‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGA  >  NC_000913/391573‑391824                                                                                                                               |                                                                                                                                 aaCTTCAGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTCTTGCGCTGACCGAATCGACTGGG‑T‑g‑ggggggc                                                                                                                         >  2:223639/1‑131 (MQ=255)     tCAGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGAGTTTACCGAATCTACTTGG‑T‑GAGGGGGCtgat                                                                                                                      >  2:156946/1‑133 (MQ=255)       aGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACtggg‑t‑g‑gg                                                                                                                              <  2:515827/122‑1 (MQ=255)       aGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACtggg‑t‑g‑gg                                                                                                                              >  1:515827/1‑122 (MQ=255)              aTCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTAc                                                                                                             >  1:48212/1‑133 (MQ=255)              aTCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAACCTACTGGG‑TGG‑GGGGGCTGATAGATCCTAc                                                                                                             >  1:184106/1‑133 (MQ=255)               tCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTAcc                                                                                                            <  1:278749/133‑1 (MQ=255)               tCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTAcc                                                                                                            >  2:344713/1‑133 (MQ=255)                    ttAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGt                                                                                                       <  2:411923/133‑1 (MQ=255)                    ttAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGt                                                                                                       <  2:102534/133‑1 (MQ=255)                         taacGGTTCTTCGCTGAACATTGGTGAAGATGGATACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAatat                                                                                                  <  2:3449/133‑1 (MQ=255)                             ggTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGac                                                                                              <  2:260620/133‑1 (MQ=255)                             ggTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGac                                                                                              >  2:254281/1‑133 (MQ=255)                             ggTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGac                                                                                              >  1:260620/1‑133 (MQ=255)                              gTTCTTCGTTGAACACTGTTGATGATGGCTTCGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGaca                                                                                             <  1:156946/133‑1 (MQ=255)                              gTTCTTCGCTTAACATTGGTGAAGATGGATACATTGATACCTATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGaca                                                                                             <  2:180414/133‑1 (MQ=255)                              gTTCTTCGCTGAACACTGGTGAAGATGGGTACGTTGATACCTATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGaca                                                                                             <  2:184106/133‑1 (MQ=255)                               ttcttcGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGatac                                                                                            <  2:48212/133‑1 (MQ=255)                               ttcttcGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGacac                                                                                            <  2:309823/133‑1 (MQ=255)                                         aaCATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑T‑G‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCg                                                                                 >  2:285541/1‑133 (MQ=255)                                              tGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGt                                                                             >  2:113012/1‑133 (MQ=255)                                                          cTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCaa                                                                 >  2:262326/1‑133 (MQ=255)                                                           tACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCaaa                                                                <  1:254281/133‑1 (MQ=255)                                                                 gATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTc                                                          >  2:2428/1‑133 (MQ=255)                                                                        atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACATAGGCCTAAGCGAAGGTATTGTTTTCCAATTCTTCCGGACTg                                                   >  2:190162/1‑133 (MQ=25)                                                                        atcatcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTCTTCCGGACTg                                                   >  2:184415/1‑133 (MQ=255)                                                                         tcatcTGACTATTAACTCCTACAGTACTGTCGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGa                                                  <  1:223639/133‑1 (MQ=255)                                                                            tcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgc                                               <  1:344713/133‑1 (MQ=255)                                                                            tcTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgc                                               >  2:442979/1‑133 (MQ=255)                                                                              tGACTATTAACTCCTTCAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccg                                             <  1:184415/133‑1 (MQ=255)                                                                                       aCTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCaa                                    >  1:513569/1‑133 (MQ=255)                                                                                                 tACTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTTAAATTGTTCCGGGCTGGGGCCGCCAGACCACCTGTgccgcc                          >  2:151969/1‑133 (MQ=18)                                                                                                   cTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgccgc                        >  2:59024/1‑133 (MQ=255)                                                                                                   cTGTTGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACG‑AATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgccgcc                       >  1:283501/1‑133 (MQ=255)                                                                                                      ttGCGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCAc                     >  1:435989/1‑133 (MQ=255)                                                                                                         cGTTGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGa                  >  2:286382/1‑133 (MQ=255)                                                                                                           ttGACCGAATCTACTGGGCG‑G‑GGGGGCAGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGACCCACCAACTGTTCCGCAGCCACCGAtt                >  2:224748/1‑133 (MQ=14)                                                                                                           ttGACCGAATCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGAtt                >  2:31170/1‑133 (MQ=255)                                                                                                                cGAATCTACTGGG‑T‑GCGGCGGCAGATTGATACTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAAt           <  1:151969/133‑1 (MQ=14)                                                                                                                   aTCTACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACG‑AATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATcaca       <  2:283501/133‑1 (MQ=255)                                                                                                                      tACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt     <  1:345757/133‑1 (MQ=255)                                                                                                                      tACTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt     <  1:2428/133‑1 (MQ=255)                                                                                                                       aCTGGG‑TGG‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTc    <  2:513569/133‑1 (MQ=255)                                                                                                                        cTGGG‑T‑G‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa  <  1:285541/133‑1 (MQ=255)                                                                                                                         tggg‑tgg‑gGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa  <  1:429137/133‑1 (MQ=255)                                                                                                                         tggg‑tgg‑gGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa  <  1:113012/133‑1 (MQ=255)                                                                                                                               |                                                                                                                                 AACTTCAGATACTATCGATTTAACTAACGGTTCTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGG‑T‑G‑GGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGA  >  NC_000913/391573‑391824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑