Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,405,012	A→G	pseudogene (281/300 nt)	yrdE →	pseudogene, yedZ paralog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,405,012	0	A	G	97.8%	169.6 / ‑4.2	46	pseudogene (281/300 nt)	yrdE	pseudogene, yedZ paralog
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (21/24);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

AATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGTT  >  NC_000913/3404873‑3405159                                                                                                                                            |                                                                                                                                                    aaTCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTcc                                                                                                                                          <  1:183876/151‑1 (MQ=255) aaTCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTc                                                                                                                                           <  2:377566/150‑1 (MQ=255)    ccccAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGt                                                                                                                                        <  1:396610/150‑1 (MQ=255)      ccAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCg                                                                                                                                      >  1:580137/1‑150 (MQ=255)         gCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCgatga                                                                                                                                  <  1:404129/151‑1 (MQ=255)           aaCCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGatgatg                                                                                                                                >  1:328600/1‑151 (MQ=255)              cGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGgcg                                                                                                                             <  2:111808/151‑1 (MQ=255)              cGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGgcg                                                                                                                             >  2:548099/1‑151 (MQ=255)                           cgtcTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGa                                                                                                                 <  2:285679/150‑1 (MQ=255)                            gtcTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAAt                                                                                                               <  1:607420/151‑1 (MQ=255)                                aTCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAAtt                                                                                                              <  2:380205/148‑1 (MQ=255)                                          gATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCttgttg                                                                                                 >  2:237335/1‑151 (MQ=255)                                             ccTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCa                                                                                               <  1:507055/150‑1 (MQ=255)                                             ccTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCa                                                                                               <  2:247965/150‑1 (MQ=255)                                                ggCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCaaa                                                                                             <  1:90011/149‑1 (MQ=255)                                                       cTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGgt                                                                                    >  1:94100/1‑151 (MQ=255)                                                         aCATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGgtgt                                                                                  >  1:250895/1‑151 (MQ=255)                                                          cATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGtt                                                                                 >  1:61770/1‑151 (MQ=255)                                                              attTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGaa                                                                              <  1:324373/150‑1 (MQ=255)                                                               tttGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAgg                                                                            >  2:135406/1‑151 (MQ=255)                                                                    ggTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTAtt                                                                       <  1:397415/151‑1 (MQ=255)                                                                    ggTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTAt                                                                        <  2:404684/150‑1 (MQ=255)                                                                           gAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGt                                                                >  2:387876/1‑151 (MQ=255)                                                                              gATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAg                                                             <  1:534571/151‑1 (MQ=255)                                                                               aTTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGc                                                            <  2:148414/151‑1 (MQ=255)                                                                                ttATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCt                                                           >  2:522660/1‑151 (MQ=255)                                                                                 tATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTg                                                          >  1:612678/1‑151 (MQ=255)                                                                                  aTCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGt                                                         >  1:478633/1‑151 (MQ=255)                                                                                     tcATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTg                                                       >  2:396795/1‑150 (MQ=255)                                                                                         tGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTAt                                                  >  1:511718/1‑151 (MQ=255)                                                                                           cAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCt                                                <  2:252894/151‑1 (MQ=255)                                                                                               cccTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCCAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTccc                                            >  2:480422/1‑151 (MQ=255)                                                                                                ccTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCt                                           <  2:419668/151‑1 (MQ=255)                                                                                                 cTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTg                                          >  1:229113/1‑151 (MQ=255)                                                                                                   cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTg                                          <  2:488240/149‑1 (MQ=255)                                                                                                   cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGa                                         <  2:528633/150‑1 (MQ=255)                                                                                                   cATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGAt                                        >  2:338941/1‑151 (MQ=255)                                                                                                                 tggctTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTAttt                           >  2:179487/1‑150 (MQ=255)                                                                                                                  ggctTTTCAGCTTTTCACCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTa                          <  1:393659/150‑1 (MQ=255)                                                                                                                         cagcttttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGACa                   <  1:387736/150‑1 (MQ=255)                                                                                                                            cttttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTg               >  1:51421/1‑151 (MQ=255)                                                                                                                               ttcaCCTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCt             <  2:194079/150‑1 (MQ=255)                                                                                                                                    cTTACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGaa        >  1:564842/1‑150 (MQ=255)                                                                                                                                     ttACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAAt      >  2:351029/1‑151 (MQ=255)                                                                                                                                      tACGTTGTAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAAt      <  1:418144/150‑1 (MQ=255)                                                                                                                                          ttATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGtt  >  2:288838/1‑150 (MQ=255)                                                                                                                                            |                                                                                                                                                    AATCCCCAGCAACCGCTGCGTAATGTCGTCTATCTTGTCGCGATCCTGGCATCCCTACATTATTTGTGGTCTGTGAAGATTATCTCATTGCAGCCCCTCATCTTCGCAGGGCTGGCTTTTCAGCTTTTCACCTTACGTTATAAGAAGTTCCGTCGATGATGGCGCTAATTTCGTGAATTGTGCGGCTTGTTGCAAATTACACGGTGTTGAAGGTTATTTACATGTTAGCTGTTGATTATCTTCCCTGATAAGACCAGTATTTAGCTGCCAATTGCTACGAAATCGTT  >  NC_000913/3404873‑3405159

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑