Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,053	(C)6→7	pseudogene (73/1461 nt)	yneO ←	pseudogene, AidA homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,047	1	.	C	96.0%	169.4 / ‑0.2	50	pseudogene (79/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (25/23);  total (26/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01

ATCAACCCGAACGCGAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTT‑CCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAT  >  NC_000913/1593898‑1594191                                                                                                                                                        |                                                                                                                                                 aTCAACCCGAACGCGAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGttt                                                                                                                                                   <  2:385208/150‑1 (MQ=255)       ccGAACGCGAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTT‑ccccccc                                                                                                                                           <  2:372182/151‑2 (MQ=255)          aaCGCGAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTT‑cccccccttc                                                                                                                                        >  2:290504/1‑147 (MQ=255)            cgcgAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGc                                                                                                                                       <  2:442185/151‑1 (MQ=255)             gcgAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCt                                                                                                                                      <  2:264201/151‑1 (MQ=255)             gcgAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCt                                                                                                                                      >  2:239839/1‑151 (MQ=255)              cgAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTa                                                                                                                                     <  1:804301/151‑1 (MQ=255)              agAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGGTTC‑CCCCCCTTCGCt                                                                                                                                      >  2:772427/2‑150 (MQ=255)               gAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTAt                                                                                                                                    >  1:803214/1‑151 (MQ=255)                 gtgtTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTc                                                                                                                                  <  1:189110/151‑1 (MQ=255)                       ccTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCAttt                                                                                                                              >  1:118656/1‑149 (MQ=255)                            ggTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGt                                                                                                                       <  2:54459/151‑1 (MQ=255)                                    cTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCAt                                                                                                               >  1:762688/1‑151 (MQ=255)                                    cTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAAGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCAt                                                                                                               >  1:38895/1‑151 (MQ=255)                                        cACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATtct                                                                                                            <  1:782933/150‑1 (MQ=255)                                         aCGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTcc                                                                                                          <  1:649141/151‑1 (MQ=255)                                            ttCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAg                                                                                                        <  2:145810/150‑1 (MQ=255)                                               aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTg                                                                                                    >  1:855939/1‑151 (MQ=255)                                                tCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTgc                                                                                                   >  2:341152/1‑151 (MQ=255)                                                  ttATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTgcc                                                                                                  >  1:211516/1‑150 (MQ=255)                                                   tATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTg                                                                                                    <  2:315014/147‑1 (MQ=255)                                                    aTCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCCTTTGAACCGCGCCGCCATTCTCCAGGCTgtcgcc                                                                                               >  1:54066/1‑151 (MQ=255)                                                    aTCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTgccgcc                                                                                               <  1:847341/151‑1 (MQ=255)                                                      cGGTGGGCGACTTATCGCTGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCTGCCATTCTCCAGGTTGccgccg                                                                                              >  2:169200/1‑150 (MQ=255)                                                      cGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGccgccg                                                                                              >  1:686865/1‑150 (MQ=255)                                                       ggTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTTATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGAt                                                                                            <  2:484992/151‑1 (MQ=255)                                                                    tCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTa                                                                                  >  2:665395/1‑148 (MQ=255)                                                                     cgccgcCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCg                                                                               >  2:280431/1‑150 (MQ=255)                                                                             aGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGt                                                                      >  2:738449/1‑151 (MQ=255)                                                                                    cgTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccccc                                                               >  1:451085/1‑151 (MQ=255)                                                                                     gTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGccccccc                                                              >  2:58341/1‑151 (MQ=255)                                                                                               atcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATaa                                                     <  1:558337/150‑1 (MQ=255)                                                                                               atcaGGCCATTGTTTCCGGTATAGTTGCCGTGAACGGACAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGGTAGTGGTTTTAGCGACACGCAGTGCCCTCCCCAGGCATaa                                                     <  2:863550/150‑1 (MQ=255)                                                                                                 caGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACg                                                   <  2:962761/150‑1 (MQ=255)                                                                                                              ccGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGc                                     >  2:622554/1‑151 (MQ=255)                                                                                                                 gTATTGTTACCGTTAACGGTCGGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGACCCGTGCCGCCATTCTCCGGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCTCCTGCAg                                   <  2:772619/150‑1 (MQ=255)                                                                                                                   ataGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAgtgg                                <  1:779746/151‑1 (MQ=255)                                                                                                                     aGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAgtggt                               <  1:443669/150‑1 (MQ=255)                                                                                                                       ttGCCGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGAc                            >  2:56764/1‑151 (MQ=255)                                                                                                                           cGTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACAttt                        >  1:408292/1‑151 (MQ=255)                                                                                                                            gTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                       <  1:290538/151‑1 (MQ=255)                                                                                                                            gTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                       <  1:529403/151‑1 (MQ=255)                                                                                                                            gTTAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCACAGGCATAACGTTCATATCACCTGCAGTGGAGACCTTTc                       >  2:354926/1‑151 (MQ=255)                                                                                                                             ttATCGGTCAGTACATTCCCCTGGTTC‑CCCCCCTTCGCTATTCATTTGACCCGTGCCGCCATCCTCCCGGTTGCCGCCGATAGTGGCTTGAGCTGCACGCAGTGCCCCCCCCAGGCATAACGTTCATATCAACTGCAGTGGTGACAt                          <  2:120944/147‑1 (MQ=255)                                                                                                                              tAACGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                      <  2:841258/150‑1 (MQ=255)                                                                                                                               aaCGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTccc                     >  1:7889/1‑150 (MQ=255)                                                                                                                                 cGGTCAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc                  >  1:465930/1‑151 (MQ=255)                                                                                                                                     cAGTACATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca              <  2:294059/151‑1 (MQ=255)                                                                                                                                         aCATTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACAcc          >  1:913660/1‑151 (MQ=255)                                                                                                                                           aTTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc        <  1:590070/151‑1 (MQ=255)                                                                                                                                           aTTCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc        >  1:779136/1‑151 (MQ=255)                                                                                                                                            ttCCCC‑GGTTTCCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCt       >  2:640688/1‑151 (MQ=255)                                                                                                                                                 c‑GGTTTCCCCCCCTTCGCTTTTCATTTGAGCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATACCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt  <  2:12955/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                 ATCAACCCGAACGCGAGTGTTCCCTTGGGTATCGCCTTTCACGTTCATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCC‑GGTTT‑CCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAT  >  NC_000913/1593898‑1594191

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑