Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,132	(C)8→9	pseudogene (3856/3861 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,124	1	.	C	91.5%	191.1 / 11.6	59	pseudogene (2/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (1/4);  new base C (28/26);  total (29/30)
Fisher's exact test for biased strand distribution p-value = 3.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATG  >  NC_000913/1594025‑1594223                                                                                                     |                                                                                                        aCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTg                                                                                                          >  1:405359/1‑100 (MQ=255) aCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTg                                                                                                          <  2:641390/100‑1 (MQ=255)        gTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCAAAAGTGGTTTTAGCGACACGCAGTG‑cc‑c‑c‑cc‑c                                                                                              >  2:1098479/1‑100 (MQ=255)        gTACATTCCCCGGGTCCCCCCCTTCGCGACTCATATGAACCGTGCCGCCATTCACCAGGTTCCCGCCGATAGTTGTTTTAGCTACACGCAGTc‑cc‑cgcgc                                                                                                 >  1:903689/1‑96 (MQ=255)          aCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAATG‑cc‑c‑c‑cc                                                                                                >  2:741212/1‑97 (MQ=255)          aCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTCAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATATTGGTTTTAGCGACACGCAGTC‑cc‑c‑c‑cc‑cc                                                                                             >  2:1445006/1‑99 (MQ=255)           cATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cc‑c‑c‑cc‑ccca                                                                                           >  1:498745/1‑98 (MQ=255)           cATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cc‑c‑c‑cc‑ccc                                                                                            >  1:1477800/1‑98 (MQ=255)             ttCCCCGTTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTTTCTTCACGCAGTG‑CC‑C‑C‑CC‑CCAGGc                                                                                         <  1:912180/100‑1 (MQ=255)               ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCa                                                                                        <  1:507281/100‑1 (MQ=255)               ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCa                                                                                        >  1:211147/1‑100 (MQ=255)               ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCa                                                                                        >  2:633035/1‑100 (MQ=255)                cccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACAAGCAGTGCCC‑C‑C‑CC‑CCAGGCAt                                                                                       >  1:222714/1‑100 (MQ=255)                 ccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGCTTGCCGCCGATAGTGGTTTTAACGACACACAATA‑CC‑CAC‑CC‑CCAg                                                                                           >  2:751837/1‑95 (MQ=255)                  cGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATaa                                                                                     <  2:211148/100‑1 (MQ=255)                    gTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACg                                                                                   <  2:1477811/100‑1 (MQ=255)                    gTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CC‑C‑C‑CCGCCAGGCATAACg                                                                                   <  2:1195628/100‑1 (MQ=255)                       tCCCCCCTTCGCTATTCATTTAAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACggt                                                                                 >  1:1324980/1‑97 (MQ=255)                        ccccccTTCGCTATTCATTTGAACCGTCCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCa                                                                               >  1:1443785/1‑100 (MQ=255)                         cccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCat                                                                              <  2:1657092/100‑1 (MQ=255)                         cccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCat                                                                              <  2:1811488/100‑1 (MQ=255)                         cccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCat                                                                              >  2:390259/1‑100 (MQ=255)                         cccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCat                                                                              <  1:224434/100‑1 (MQ=255)                          ctccTTCGCTATTCATTTGAACCTTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGTTTTTAGCGACACGCAGTG‑CC‑C‑CTCC‑CCAGGCATAACGTTc                                                                                <  1:1225717/95‑1 (MQ=255)                          ccccTTCGCTATTCATTTGAACCGTGTCGCCATTTTCCAGGTTGCCGCCGATATTGGTTTTAGCGACATGCAGTG‑CCTC‑C‑CC‑CCAGGCATAACGTTCata                                                                             <  1:814040/100‑1 (MQ=255)                          ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCata                                                                             <  1:9411/100‑1 (MQ=255)                             cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCa                                                                          >  1:1549141/1‑100 (MQ=255)                                  cTATTCTTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGc                                                                     <  2:1046396/100‑1 (MQ=255)                                   tATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGc                                                                     >  1:901425/1‑99 (MQ=255)                                       cATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCCGACATAACATTCATATCACCTACa                                                                    >  2:504720/1‑96 (MQ=255)                                        aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAgtggt                                                               >  1:805105/1‑100 (MQ=255)                                         tttGAACCGTGCCGCCATTCTCCAGGTTGCTGCCTATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAgtggtg                                                              <  2:662112/100‑1 (MQ=255)                                         tttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAgtggtg                                                              >  2:308959/1‑100 (MQ=255)                                         tttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAgtggtg                                                              <  1:1214539/100‑1 (MQ=255)                                         tttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAgtggtg                                                              <  1:622517/100‑1 (MQ=255)                                          ttGAACCGTGCCGCTATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                             <  2:1044354/100‑1 (MQ=255)                                          ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                             >  2:1411612/1‑100 (MQ=255)                                          ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCACTGGTGa                                                             >  2:846710/1‑100 (MQ=255)                                           tGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                             >  2:1016005/1‑99 (MQ=255)                                           tGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGAc                                                            <  1:865379/100‑1 (MQ=255)                                           tGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAATGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGAc                                                            >  1:1583881/1‑100 (MQ=255)                                                 gTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                      <  2:405361/100‑1 (MQ=255)                                                 gTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                      <  1:1162421/100‑1 (MQ=255)                                                  tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTccc                                                     <  2:54185/100‑1 (MQ=255)                                                   gccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg                                                    <  1:1557155/100‑1 (MQ=255)                                                    ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                   >  2:378540/1‑100 (MQ=255)                                                        cATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATc                                               <  2:1020422/100‑1 (MQ=255)                                                            ctcCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                           >  2:1512413/1‑100 (MQ=255)                                                                 ggTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCt                                       >  2:182451/1‑99 (MQ=255)                                                                   ttGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                    <  1:1098469/100‑1 (MQ=255)                                                                        gccgATAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGa                               <  1:490425/100‑1 (MQ=255)                                                                             tAGTGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTa                          >  2:498494/1‑100 (MQ=255)                                                                                tGGTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtg                       <  1:314798/100‑1 (MQ=255)                                                                                 ggTTTTAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGGGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtgt                      >  1:1352315/1‑100 (MQ=255)                                                                                   ttttAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATgtgt                    <  1:651214/100‑1 (MQ=255)                                                                                   ttttAGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATgtgt                    >  2:1774229/1‑100 (MQ=255)                                                                                       aGCGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc                >  1:176237/1‑100 (MQ=255)                                                                                         cGACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACtt              >  2:921189/1‑100 (MQ=255)                                                                                          gACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTg             >  1:705268/1‑100 (MQ=255)                                                                                          gACACGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGACGCGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc                >  2:1062925/1‑97 (MQ=255)                                                                                            cacGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc           <  1:142118/100‑1 (MQ=255)                                                                                            cacGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGGGGTGACATTTCCCGACCTCACACCGCTGTTTAGGATTTTTATGTTTTGACtttc            >  2:1712138/1‑97 (MQ=255)                                                                                            cacGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTAATATTACCTGCAGTGGAGACATTTCCCCACATCACAACGCTGTTATGGATATTAATTTGTTTACTTAcc           >  1:122758/1‑100 (MQ=255)                                                                                             acGCAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCa          <  1:308957/100‑1 (MQ=255)                                                                                              cGCAGTGCCC‑C‑C‑CC‑CCAGGCATACCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat         <  1:467519/100‑1 (MQ=255)                                                                                                cAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATTGATATTAATGTGTTGACTTGCCata        >  1:713993/1‑99 (MQ=255)                                                                                                cAGTGCCC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCatat       <  1:378538/100‑1 (MQ=255)                                                                                                    g‑CC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATg  >  1:1596570/1‑100 (MQ=255)                                                                                                     |                                                                                                        ACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CC‑C‑C‑CC‑CCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATG  >  NC_000913/1594025‑1594223

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑