Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,572,919	A→T	pseudogene (506/1503 nt)	yjiT →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,572,919	0	A	T	98.4%	221.1 / ‑4.1	64	pseudogene (506/1503 nt)	yjiT	pseudogene
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base T (30/33);  total (30/34)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.07e-01

AGTGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCAGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGAACTTATCA  >  NC_000913/4572822‑4573014                                                                                                  |                                                                                                aGTGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCTAGGATCCTTGGACAATATGAGCAAGCAAAGCTGt                                                                                               >  2:254462/1‑100 (MQ=255)  gTGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTc                                                                                              >  1:506209/1‑100 (MQ=255)  gTGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTc                                                                                              <  2:1172417/100‑1 (MQ=255)   tGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCa                                                                                             <  1:1271839/100‑1 (MQ=255)    gAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAg                                                                                            >  1:817886/1‑100 (MQ=255)    gAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAg                                                                                            >  1:899450/1‑100 (MQ=255)      nggtggtTTACCTTTCCGGCTACTCAAATAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGt                                                                                          >  2:191457/2‑100 (MQ=255)       ggtggtTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGtt                                                                                         <  1:913088/100‑1 (MQ=255)           gtTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGttttt                                                                                      <  2:870174/99‑1 (MQ=255)           gtTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTc                                                                                     >  1:461662/1‑100 (MQ=255)           gtTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTc                                                                                     <  1:540033/100‑1 (MQ=255)            tttACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCt                                                                                    >  2:42538/1‑100 (MQ=255)             ttACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTg                                                                                   <  2:23244/100‑1 (MQ=255)              tACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCt                                                                                    >  2:1123757/1‑98 (MQ=255)                 cTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCt                                                                               >  1:474765/1‑100 (MQ=255)                  tttCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCtt                                                                              >  1:862267/1‑100 (MQ=255)                      cGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGc                                                                          >  1:423974/1‑100 (MQ=255)                       ggCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCt                                                                         >  2:575515/1‑100 (MQ=255)                       ggCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCt                                                                         >  1:489940/1‑100 (MQ=255)                        gCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTg                                                                        <  1:335470/100‑1 (MQ=255)                        gCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCATTTCGCTg                                                                        <  1:1123767/100‑1 (MQ=255)                         cTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTgg                                                                       >  1:650348/1‑100 (MQ=255)                         cTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTgg                                                                       <  1:842379/100‑1 (MQ=255)                           aCTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCa                                                                     <  1:476183/100‑1 (MQ=255)                            ctaaaaGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAGAGCTGTCAGGATTTTGTGCCCTTTTGCTGGCaa                                                                    >  2:555345/4‑100 (MQ=255)                             tCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAag                                                                   >  2:333256/1‑100 (MQ=255)                              cAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAaga                                                                  >  2:998204/1‑100 (MQ=255)                              cAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAaga                                                                  >  1:432139/1‑100 (MQ=255)                              cAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAaga                                                                  >  2:18167/1‑100 (MQ=255)                                aaGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGc                                                                <  1:942337/100‑1 (MQ=255)                                    aTCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTc                                                            >  2:1130357/1‑100 (MQ=255)                                       aGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATa                                                         >  1:1249008/1‑100 (MQ=255)                                          cAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGa                                                       <  1:1030450/99‑1 (MQ=255)                                                cTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCa                                                >  2:749674/1‑100 (MQ=255)                                                cTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCAGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCa                                                <  2:161046/100‑1 (MQ=255)                                                   tCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAgcg                                             <  2:489068/100‑1 (MQ=255)                                                      ggCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAgcgaga                                          >  1:489072/1‑97 (MQ=255)                                                      ggCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTg                                          <  1:851518/100‑1 (MQ=255)                                                       gCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGc                                         <  1:348393/100‑1 (MQ=255)                                                       gCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGc                                         >  2:719735/1‑100 (MQ=255)                                                       gCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGc                                         >  1:1209626/1‑100 (MQ=255)                                                        cTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGcc                                        >  1:743048/1‑100 (MQ=255)                                                              tctcCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGt                                  <  2:474761/100‑1 (MQ=255)                                                               ctcCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGTCAAGAGCTGTCATAGAAATATCAGCGCTGCCAACTGtt                                 <  2:776897/100‑1 (MQ=255)                                                               ctcCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGtt                                 >  1:740210/1‑100 (MQ=255)                                                               ctcCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGtt                                 <  1:1178825/100‑1 (MQ=255)                                                                tcCAGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGttt                                <  2:405997/100‑1 (MQ=255)                                                                   aGGATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTa                             <  2:1163903/100‑1 (MQ=255)                                                                     gATCCTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGc                           <  1:1130809/100‑1 (MQ=255)                                                                         cTTGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTCTTTTTAGCGAAg                       <  1:529230/100‑1 (MQ=255)                                                                          ttGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGa                      <  1:42539/100‑1 (MQ=255)                                                                          ttGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGa                      <  2:497208/100‑1 (MQ=255)                                                                           tGGACAATATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGAt                     <  1:333259/100‑1 (MQ=255)                                                                                aaTATGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACctc                <  1:549801/100‑1 (MQ=255)                                                                                  tatGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTg              <  2:422721/100‑1 (MQ=255)                                                                                  tatGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTg              <  2:753139/100‑1 (MQ=255)                                                                                  tatGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTg              >  2:67461/1‑100 (MQ=255)                                                                                    ttagcaagcaAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTa            <  2:209044/98‑1 (MQ=255)                                                                                    tGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTa            <  1:263935/100‑1 (MQ=255)                                                                                    tGAGCAAGCAAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTa            >  2:211315/1‑100 (MQ=255)                                                                                    tGAGCAAGCAAAGCTGTCAGGTGTTGCTGCCGTTGCGCTGGAAAGAGCTGTCATAGAAAAATCAGCGCTGGCAACTGTTTTTAGCGAAGATACCTCTGTa            <  2:80925/100‑1 (MQ=255)                                                                                      agcaagcaAAGCTGTCAGGTTTTTTTTTTTTTTTTCTGGCAAAAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGa          >  2:189071/1‑100 (MQ=255)                                                                                      agcaagcaAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGa          <  2:573284/100‑1 (MQ=255)                                                                                      agcaagcaAAGCTGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGa          <  1:590179/100‑1 (MQ=255)                                                                                           gcaaagctGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGAACTTa     <  1:361724/100‑1 (MQ=255)                                                                                             aaagcaGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGAACTTATc   <  2:282492/100‑1 (MQ=255)                                                                                              aagctGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGAACTTATCa  >  2:1229713/1‑100 (MQ=255)                                                                                                  |                                                                                                AGTGAAGGTGGTTTACCTTTCCGGCTACTCAAAGAATCAGACAGTCGCTTTCTGGCTGTTTTCTCCAGGATCCTTGGACAATATGAGCAAGCAAAGCAGTCAGGTTTTTCTGCCCTTTCGCTGGCAAGAGCTGTCATAGAAAAATCAGCGCTGCCAACTGTTTTTAGCGAAGATACCTCTGTAGAACTTATCA  >  NC_000913/4572822‑4573014

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑