Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,210,811	C→T	pseudogene (1712/2001 nt)	yehQ →	pseudogene

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,210,811	0	C	T	97.3%	253.0 / ‑1.9	75	pseudogene (1712/2001 nt)	yehQ	pseudogene
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (31/42);  total (32/43)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.15e-01

GTCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACG  >  NC_000913/2210714‑2210903                                                                                                  |                                                                                             gTCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGc                                                                                            <  2:304323/100‑1 (MQ=255)     gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAcc                                                                                        >  1:558520/1‑100 (MQ=255)     gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAcc                                                                                        >  1:1416181/1‑100 (MQ=255)     gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAcc                                                                                        <  1:727479/100‑1 (MQ=255)        ttgttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTc                                                                                     >  2:1317128/1‑100 (MQ=255)         tgttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAGCCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCt                                                                                    <  2:1992992/100‑1 (MQ=255)         tgttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCt                                                                                    >  2:902192/1‑100 (MQ=255)           ttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGc                                                                                  <  1:1423572/100‑1 (MQ=255)           ttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGc                                                                                  >  1:1627560/1‑100 (MQ=255)            tgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGcc                                                                                 >  2:676352/1‑100 (MQ=255)            tgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGcc                                                                                 <  1:261134/100‑1 (MQ=255)            tgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGcc                                                                                 >  2:1417674/1‑100 (MQ=255)              aaGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAg                                                                               <  1:1208891/100‑1 (MQ=255)               aGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGc                                                                              >  2:941701/1‑100 (MQ=255)               aGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGc                                                                              <  1:237234/100‑1 (MQ=255)                gggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCg                                                                             >  2:1578496/1‑100 (MQ=255)                gggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCg                                                                             <  2:161443/100‑1 (MQ=255)                gggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCg                                                                             >  1:543824/1‑100 (MQ=255)                   cAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGttt                                                                          <  1:1013346/100‑1 (MQ=255)                     aTTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTg                                                                        >  2:1494976/1‑100 (MQ=255)                     aTTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTg                                                                        <  1:1454229/100‑1 (MQ=255)                      ttGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGc                                                                       <  1:331291/100‑1 (MQ=255)                       tGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGcc                                                                      <  1:428277/100‑1 (MQ=255)                       ccgatcTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGcc                                                                      <  1:2005812/95‑1 (MQ=255)                            cTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGc                                                                 >  1:744504/1‑100 (MQ=255)                              ggAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGccagatcgg                                                               >  2:2005794/1‑93 (MQ=255)                              ggAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCg                                                               <  1:725857/100‑1 (MQ=255)                                  ccACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTa                                                           <  1:749859/100‑1 (MQ=255)                                   cACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCATTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTAc                                                          <  2:1094711/100‑1 (MQ=255)                                   cACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTAc                                                          <  1:902195/100‑1 (MQ=255)                                    aCGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACt                                                         <  2:1175686/100‑1 (MQ=255)                                      gggTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGc                                                       <  1:676354/100‑1 (MQ=255)                                      gggTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGc                                                       <  2:256983/100‑1 (MQ=255)                                      gggTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGc                                                       <  1:941705/100‑1 (MQ=255)                                       ggTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCt                                                      >  2:1033908/1‑100 (MQ=255)                                        gTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCtc                                                     <  2:558518/100‑1 (MQ=255)                                            ttatgaCAAAAACACGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCtcatca                                                 >  1:1384531/3‑100 (MQ=255)                                            tgatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCtcatca                                                 <  1:338573/100‑1 (MQ=255)                                            tgatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCtcatca                                                 <  1:1696754/100‑1 (MQ=255)                                             gatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAg                                                >  1:1503450/1‑100 (MQ=255)                                             gatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAg                                                >  2:651453/1‑100 (MQ=255)                                             gatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACCACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAg                                                <  2:289889/100‑1 (MQ=255)                                               tgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGtt                                              >  2:1439718/1‑100 (MQ=255)                                               tgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGtt                                              >  1:1834718/1‑100 (MQ=255)                                               tgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGtt                                              >  1:351594/1‑100 (MQ=255)                                               tcaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGtt                                              >  1:1891702/3‑100 (MQ=255)                                                 aCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTg                                             <  2:719394/99‑1 (MQ=255)                                                 aCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGc                                            >  1:1093607/1‑100 (MQ=255)                                                  cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                           <  2:1120335/100‑1 (MQ=255)                                                  cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                           <  2:187156/100‑1 (MQ=255)                                                     aaaCCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGAt                                        <  1:1804890/100‑1 (MQ=255)                                                       aCCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATAc                                      <  1:1944751/100‑1 (MQ=255)                                                          cGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCt                                   >  2:706986/1‑100 (MQ=255)                                                            tGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGc                                 <  1:771200/100‑1 (MQ=255)                                                              ccTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCa                               <  1:1770737/100‑1 (MQ=255)                                                               cTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAg                              <  2:341623/100‑1 (MQ=255)                                                                  ggCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCg                           <  1:964490/100‑1 (MQ=255)                                                                  ggCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCg                           >  2:799246/1‑100 (MQ=255)                                                                  cccgcTGGACGCAGAAACTACTCCGGTGGCACTGCTACCGCCTGCCAGCTTGTTGCCTGTGCCGTCGACTGCGCATCAGTTGCTGAGACGCTGCCAg                              >  2:167849/3‑97 (MQ=255)                                                                   gcgcTTGGCGCAGAAGCTACGCCTGTGGCACTGCTACCTTCTGCCAGCGGTTTGCCGGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGcc                                <  2:1834702/94‑1 (MQ=255)                                                                    cgcTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGtt                         <  1:1494985/100‑1 (MQ=255)                                                                      cTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTAc                       <  1:1417683/100‑1 (MQ=255)                                                                      cTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTAc                       <  2:1395112/100‑1 (MQ=255)                                                                         gACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTa                    >  2:220678/1‑100 (MQ=255)                                                                         gACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTa                    <  1:1578506/100‑1 (MQ=255)                                                                           cGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTAtt                  >  1:93589/1‑100 (MQ=255)                                                                            gCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTAttn                 <  2:1770626/100‑2 (MQ=255)                                                                             cAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCa                >  2:1479914/1‑100 (MQ=255)                                                                             cAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCa                >  1:1550104/1‑100 (MQ=255)                                                                             cAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCa                <  1:1479923/100‑1 (MQ=255)                                                                             cAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCa                >  2:1689766/1‑100 (MQ=255)                                                                                 aaCTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTg            >  2:1654741/1‑100 (MQ=255)                                                                                          tgtgGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAAc   >  1:1665858/1‑100 (MQ=255)                                                                                          tgtgGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGGCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAAc   <  2:543823/100‑1 (MQ=255)                                                                                           gtgGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACg  <  1:1033913/100‑1 (MQ=255)                                                                                                  |                                                                                             GTCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACG  >  NC_000913/2210714‑2210903

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑