Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,210,811	C→T	100%	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	96.6%	236.9 / ‑1.8	77	pseudogene (1712/2001 nt)	yehQ	pseudogene
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base T (40/34);  total (42/35)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTG  >  NC_000913/2210715‑2210907                                                                                                 |                                                                                                 tCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCt                                                                                               <  1:805724/100‑1 (MQ=255)    gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAcc                                                                                            >  1:1989351/1‑100 (MQ=255)    gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAc                                                                                             >  1:55613/1‑99 (MQ=255)    gTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGAGGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTAcc                                                                                            <  1:381713/100‑1 (MQ=255)     ttttGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCt                                                                                           <  2:1517007/100‑1 (MQ=255)         gttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCt                                                                                        >  2:2247798/1‑99 (MQ=255)         gttgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTg                                                                                       >  1:957437/1‑100 (MQ=255)           tgAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGcc                                                                                     >  2:2020425/1‑100 (MQ=255)            gAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCa                                                                                    >  1:1330103/1‑100 (MQ=255)             aaGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAg                                                                                   >  1:1823029/1‑100 (MQ=255)              aGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAg                                                                                   >  2:981977/1‑99 (MQ=255)               gggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGc                                                                                  >  1:205673/1‑99 (MQ=255)                ggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGt                                                                                >  1:1444785/1‑100 (MQ=255)                ggCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGt                                                                                <  1:1798431/100‑1 (MQ=255)                  cAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGttt                                                                              >  1:769743/1‑100 (MQ=255)                   atctGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGtttt                                                                             <  1:1890266/97‑1 (MQ=255)                     ttGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGc                                                                           <  1:431668/100‑1 (MQ=255)                      tGACACTGGCACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGTACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGcc                                                                          <  2:632442/100‑1 (MQ=255)                      tGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCATTGCTATCTTCTGCCAGCGTTTTGcc                                                                          <  2:845779/100‑1 (MQ=255)                       gACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGttttagat                                                                         >  2:1890244/1‑96 (MQ=255)                       gACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCt                                                                         >  2:766604/1‑100 (MQ=255)                        acacTTGAACCACGTGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCtg                                                                        <  1:767641/100‑1 (MQ=255)                        acacTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGcc                                                                          <  1:1481163/98‑1 (MQ=255)                        acacTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCtg                                                                        <  1:1081154/100‑1 (MQ=255)                        acacTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCtg                                                                        <  2:271151/100‑1 (MQ=255)                        acacTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCtg                                                                        <  1:2082048/100‑1 (MQ=255)                           cTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGc                                                                     >  2:2021437/1‑100 (MQ=255)                           cTGGAACCACGGGTGATGATGACAAAAACCAGTACCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTGTTGCCTGTGc                                                                     >  2:1575145/1‑100 (MQ=255)                               aaCCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTc                                                                 <  2:1444770/100‑1 (MQ=255)                                aCCACGGGTGATGATGGCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCt                                                                <  1:472389/100‑1 (MQ=255)                                aCCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCt                                                                >  1:1510256/1‑100 (MQ=255)                                  cACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTAc                                                              >  2:20573/1‑100 (MQ=255)                                  cACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTAAGACTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGGCTAc                                                              >  2:2085724/1‑100 (MQ=255)                                      ngTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCt                                                          >  1:1567697/2‑100 (MQ=255)                                      ggTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCt                                                          >  2:1835356/1‑100 (MQ=255)                                           tgatgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCtcatca                                                     >  1:523377/1‑100 (MQ=255)                                             atgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGt                                                   <  2:55612/100‑1 (MQ=255)                                             atgaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGt                                                   >  1:1091528/1‑100 (MQ=255)                                               gaCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTg                                                 >  2:1990811/1‑100 (MQ=255)                                                aCAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGc                                                >  1:1408761/1‑100 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               >  1:403686/1‑100 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               >  2:2217223/1‑100 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               >  1:1305815/1‑100 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               <  2:1191787/100‑1 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               <  1:795931/100‑1 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               <  1:2170404/100‑1 (MQ=255)                                                 cAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCt                                               >  2:1190520/1‑100 (MQ=255)                                                    aaaCCCGTGCCTGGGCGTTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGan                                            <  1:1081985/100‑2 (MQ=255)                                                    aaaCCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGAt                                            <  1:1275791/100‑1 (MQ=255)                                                      aCCCGTGCCTGGGCGCTGGACGTAGAAACTACGCCTGTGGCACTGCTACCTTCTGCTAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGAt                                            <  2:2335654/98‑1 (MQ=255)                                                          gTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTg                                      <  1:1190531/100‑1 (MQ=255)                                                             ccTGGGCGCTGGACGCAGAAACTGCGCCTGTGGCACCGCTACCTTCTGCCAGCGTTCTGCCTGTGCCGTCTACCGCTCATCAGTTGCTGATGCGCTGCCa                                   >  2:481806/1‑100 (MQ=255)                                                             ccTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCCTCAGTTGCTGATACGCTGc                                     >  1:1576364/1‑98 (MQ=255)                                                             ccTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCa                                   >  1:1438545/1‑100 (MQ=255)                                                             ccTGGGCGCTGGACGCAGAAACTACGCCTGTGGCAATACTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGcaa                                   <  2:1396116/100‑3 (MQ=255)                                                                gggCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGc                                >  2:65754/1‑100 (MQ=255)                                                                gggCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGc                                <  1:1157828/100‑1 (MQ=255)                                                                gggCGCTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGc                                <  1:121730/100‑1 (MQ=255)                                                                  gcgcTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCg                               >  2:689531/1‑99 (MQ=255)                                                                   cgcTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGtt                             >  1:1760653/1‑100 (MQ=255)                                                                     cTGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTAc                           >  2:650987/1‑100 (MQ=255)                                                                     atctaCGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTAc                           <  1:1139577/96‑1 (MQ=255)                                                                      tGGACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACt                          <  2:774929/100‑1 (MQ=255)                                                                       ggACGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACtt                         >  1:259006/1‑100 (MQ=255)                                                                         aCGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTAcagat                       >  2:1139566/1‑96 (MQ=255)                                                                         aCGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTAt                       <  1:2021459/100‑1 (MQ=255)                                                                         aCGCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTAt                       <  1:1905598/100‑1 (MQ=255)                                                                           gCAGAAACTACGCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTc                     <  2:1952968/100‑1 (MQ=255)                                                                             ataaaCTACGCCTGCGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCa                    <  1:2364508/97‑1 (MQ=255)                                                                                aaCTACGCCTGTGGCACTGCTACATACTGCCAGCCTTTTGCCTGTCCCGTCTACTGCTCATCAGTAGATATAACGCTACCAGGCGTTACTTATTCAACt                 >  2:183009/1‑99 (MQ=255)                                                                                     agCCTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCa           >  1:1039301/2‑100 (MQ=255)                                                                                       ccggtgGCACTGCGACCTTCTGCCAGCGTTTTGCCTGTGCCTTGTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCAt          <  2:227726/96‑1 (MQ=255)                                                                                       ccTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATa         <  2:1647718/100‑1 (MQ=255)                                                                                        cTGTGGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGACAGGAGTTACTTATTCAACTGCTCCATaa        >  1:602288/1‑100 (MQ=255)                                                                                         tttgGCACTGCTAACTTCTGCCAGCGTTTTGGCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAAc       >  1:1613892/3‑100 (MQ=255)                                                                                           tgGCACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACgg     <  1:2020447/100‑1 (MQ=255)                                                                                              cACTGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTg  >  1:2388439/1‑100 (MQ=255)                                                                                                 |                                                                                                 TCAGTTTTGTTGAAGGGCAATTGACACTGGAACCACGGGTGATGATGACAAAAACCCGTGCCTGGGCGCTGGACGCAGAAACTACGCCTGTGGCACCGCTACCTTCTGCCAGCGTTTTGCCTGTGCCGTCTACTGCTCATCAGTTGCTGATACGCTGCCAGGCGTTACTTATTCAACTGCTCCATAACGGCTG  >  NC_000913/2210715‑2210907

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑