Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,256	(C)8→9	pseudogene (3831/5422 nt)	yneO ←	AIDA‑I family autotransporter YneO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,248	1	.	C	88.5%	162.1 / 13.4	52	pseudogene (3839/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (1/5);  new base C (32/14);  total (33/19)
Fisher's exact test for biased strand distribution p-value = 2.02e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGTGG  >  NC_000913/1594111‑1594380                                                                                                                                           |                                                                                                                                        aGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cc‑c                                                                                                                                     <  1:17807/140‑1 (MQ=255)     acacGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cc‑ccc‑cc                                                                                                                                <  1:516603/140‑1 (MQ=255)        cGCAGTG‑CCCCCCCAGGCATAAGGTTCATATGACCTGCATTGGTGACACTTCACGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cc‑ccc‑ccccg                                                                                                                             <  2:306676/140‑3 (MQ=255)        cGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑cc‑ccc‑cccca                                                                                                                             <  2:45591/140‑3 (MQ=255)               gcccccccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGatat                                                                                                                       <  2:202044/139‑1 (MQ=255)                     ccAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCcgtcg                                                                                                                 <  1:738338/140‑1 (MQ=255)                        ggCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTAc                                                                                                              >  2:604590/1‑140 (MQ=255)                             aaCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGa                                                                                                         >  2:100828/1‑140 (MQ=255)                              aCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGAt                                                                                                        <  1:100828/140‑1 (MQ=255)                                   cATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CC‑CCC‑CTC‑ACGATATCCGTCGTACCCTGATAcgccg                                                                                                  >  1:43972/1‑140 (MQ=255)                                    atatCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATAcgccg                                                                                                  >  1:125931/1‑140 (MQ=255)                                         aCCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGaa                                                                                             >  1:496130/1‑140 (MQ=255)                                          ccTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAAt                                                                                            >  1:655122/1‑140 (MQ=255)                                           cTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATc                                                                                           <  2:496130/140‑1 (MQ=255)                                            tGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCg                                                                                          >  1:510936/1‑140 (MQ=255)                                                gtggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACCATATCCGACGTCCCATGATACACCGCGGAATCgttgt                                                                                      >  1:402215/1‑140 (MQ=255)                                                       cATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGt                                                                               <  1:455819/140‑1 (MQ=255)                                                          ttCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAg                                                                            <  1:604590/140‑1 (MQ=255)                                                                           cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTGGTTTAGGGTCAGGATCCCGGTACCCAGtt                                                           >  1:230029/1‑140 (MQ=255)                                                                           cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTCGTTAAGTGTCAGGGTCCCGGTACCCAGtt                                                           >  1:247077/1‑140 (MQ=255)                                                                           cTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCAGAATCGTAGTTTAGAGTCAGGATCCCGGTACCCAGtt                                                           >  1:268896/1‑140 (MQ=255)                                                                            tGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCg                                                                     >  1:3288/1‑129 (MQ=255)                                                                            tGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCg                                                                     <  2:3288/129‑1 (MQ=255)                                                                                     tatTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATc                                                 >  2:722162/1‑140 (MQ=255)                                                                                     tatTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTAGTTGAGATTCAGGATCGCGGTGCCCAGTTTTGTCACATc                                                 >  2:259084/1‑140 (MQ=255)                                                                                        tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCacc                                              >  2:596154/1‑140 (MQ=255)                                                                                        tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGACAGGATCCCGGTACCCAGTTTTGTCACATCacc                                              >  1:560836/1‑140 (MQ=255)                                                                                           tgtgTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                           <  1:596154/140‑1 (MQ=255)                                                                                           tgtgTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                           <  2:510936/140‑1 (MQ=255)                                                                                              gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctacc                                        >  1:610736/1‑140 (MQ=255)                                                                                              gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctaccg                                       <  1:83365/140‑1 (MQ=255)                                                                                               ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCTAATTTTCTCACATCaccgctaccg                                       >  2:326532/1‑140 (MQ=255)                                                                                               ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctaccg                                       >  2:827731/1‑140 (MQ=255)                                                                                               ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                             <  1:529144/134‑1 (MQ=255)                                                                                               ttGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGGCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                             >  2:529144/1‑134 (MQ=255)                                                                                                    ttGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CC‑CCC‑CTC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATa                                 <  2:43972/140‑1 (MQ=255)                                                                                                     tGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATa                                 <  2:125931/140‑1 (MQ=255)                                                                                                     tGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTCTGACACATCGCCGCTACCGCTGATa                                 >  1:340399/1‑140 (MQ=255)                                                                                                       ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACt                               >  2:513846/1‑140 (MQ=255)                                                                                                       ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACt                               >  2:168479/1‑140 (MQ=255)                                                                                                         atatTAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTTCCCAGTTTTGTAACGTCACCGATACCGCTGATACtgt                             >  1:274567/1‑140 (MQ=255)                                                                                                            ttAATGGCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCg                          >  2:130480/1‑140 (MQ=255)                                                                                                                 ggCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTGTGTCACACCACCGCAACCGCTGATACTGTGCGTCATc                     >  1:261140/1‑140 (MQ=255)                                                                                                                 ggCAGAGTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGGCGTACCCTAATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATc                     >  2:80633/1‑140 (MQ=255)                                                                                                                      agTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa                >  2:427236/1‑140 (MQ=255)                                                                                                                      agTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa                >  2:3281/1‑140 (MQ=255)                                                                                                                      agTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa                >  2:541901/1‑140 (MQ=255)                                                                                                                      agTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa                >  2:566467/1‑140 (MQ=255)                                                                                                                      agTCGGAACCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa                >  2:709376/1‑140 (MQ=255)                                                                                                                       gTCGGAACCGAAAGCAATTT‑CCTCCC‑CCC‑ACGATATCCGGCGTACCCTTATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAg               <  2:274567/140‑1 (MQ=255)                                                                                                                       gTCGGAACCGAAAGCAATTT‑CC‑CCCACCC‑GCGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAg               <  1:262259/140‑1 (MQ=255)                                                                                                                            aaCCGAAAGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg          <  1:130480/140‑1 (MQ=255)                                                                                                                                 aaaGCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACACCACCGCTCCCGCTGAAACTTTGGGTCATCCCCCAGCTACGCTCAg     >  1:301802/1‑140 (MQ=255)                                                                                                                                    gCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGTgg  <  1:709376/140‑1 (MQ=255)                                                                                                                                    gCAATTTCCC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGTgg  <  1:722162/140‑1 (MQ=255)                                                                                                                                    gCAATTT‑CC‑CCC‑CCCGACGATATCCTTCGTACCCTGACACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGTgg  <  1:259084/140‑1 (MQ=255)                                                                                                                                           |                                                                                                                                        AGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑CC‑CCC‑CCC‑ACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAGTGG  >  NC_000913/1594111‑1594380

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑