Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,132	(C)8→9	pseudogene (3955/5422 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	1,594,124	1	.	C	92.3%	113.0 / 3.4	39	pseudogene (3963/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (2/1);  new base C (11/25);  total (13/26)
Fisher's exact test for biased strand distribution p-value = 2.53e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.11e-01

TCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGG  >  NC_000913/1593993‑1594233                                                                                                                                     |                                                                                                                tcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cccc‑cccc                                                                                                        <  2:108763/140‑1 (MQ=255)       cATTGTTTCCGGTATCGTTGCCTTTAACGATCAGTACCTTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCa                                                                                                   <  1:250292/140‑1 (MQ=255)       cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCa                                                                                                   <  2:581047/140‑1 (MQ=255)       cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cc                                                                                                               <  2:599872/128‑1 (MQ=255)       cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cc                                                                                                               >  1:599872/1‑128 (MQ=255)       cATTGTTCCCGGTTTAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCa                                                                                                   <  2:167347/140‑1 (MQ=255)         ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTCGCCGCCGAGAGTCGTTTTAGCGACAGGCAGTGCCCCC‑CCCCAGGCATa                                                                                                 >  2:267708/1‑140 (MQ=255)         ttGTTTCCGGTATAGTTGCCGTCAAAGGTGAGTACATACCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATa                                                                                                 <  1:376682/140‑1 (MQ=255)          tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTGCTCCCTTCGCTATTCATTTGAACCGTCCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATaa                                                                                                >  2:502104/1‑140 (MQ=255)                 ggTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCat                                                                                         <  2:672823/140‑1 (MQ=255)                         tGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTg                                                                                 <  2:174641/140‑1 (MQ=255)                             gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgt                                                                             >  2:671746/1‑140 (MQ=255)                               tAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgtgg                                                                           >  1:852809/1‑140 (MQ=255)                                        gTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGc                                                                                <  2:763571/126‑1 (MQ=255)                                        gTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGc                                                                                >  1:763571/1‑126 (MQ=255)                                          aCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTccc                                                                <  1:561257/140‑1 (MQ=255)                                             ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATGACCTGCAGTAGTGACATTTCCCGAc                                                             >  1:368378/1‑140 (MQ=255)                                              tCCCCGGTTTCCCCCTTTCGCTTTTCATTTGAACCGTACCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa                                                            <  1:348071/140‑1 (MQ=255)                                              tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCACCCCAGGCGTAAGGTTCATATCACCGGCAGCGGTGACATTTCCCGACa                                                            >  2:348071/1‑140 (MQ=255)                                                   ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCGGGCATAACTTTCGTATGACCTGCAGTGGTGACATTTCCCGACATcaca                                                       >  2:229712/1‑140 (MQ=255)                                                      ttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                    <  2:852809/140‑1 (MQ=255)                                                             ctccGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                             <  2:630380/137‑1 (MQ=255)                                                             cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                             <  1:671746/140‑1 (MQ=255)                                                               tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                    <  1:722654/131‑1 (MQ=255)                                                               tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                    >  2:722654/1‑131 (MQ=255)                                                                cGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGa                                          >  1:642695/1‑140 (MQ=255)                                                                    aTTCATTTGACCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TAtt                                     <  1:164573/140‑1 (MQ=255)                                                                    aTTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TAtt                                     <  2:508635/140‑1 (MQ=255)                                                                             aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTa                                    >  2:115399/1‑131 (MQ=255)                                                                             aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTa                                    <  1:115399/131‑1 (MQ=255)                                                                               ccGTGCCGCCATTCTGCAGGTTTCCCCCGTTAGTGGTCTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGAc                          <  1:229712/140‑1 (MQ=255)                                                                               ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGAc                          >  1:866033/1‑140 (MQ=255)                                                                               ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGAc                          <  1:682820/140‑1 (MQ=255)                                                                               ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGAc                          <  1:675533/140‑1 (MQ=255)                                                                                cGTGCCGCCATTCTCCAGGTTGTCGCCGATAGTGGGTTTCGCGACACGAAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACt                         <  2:368378/140‑1 (MQ=255)                                                                                cGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACt                         <  1:500683/140‑1 (MQ=255)                                                                                  tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTg                       >  1:477622/1‑140 (MQ=255)                                                                                    ccgccATTCTCCAGGTTTCCGCCAATAGTGGGTTTAGCGCCACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGcc                     <  2:336617/140‑1 (MQ=255)                                                                                    ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGcc                     <  2:866033/140‑1 (MQ=255)                                                                                    ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGcc                     <  1:502104/140‑1 (MQ=255)                                                                                    ccgccATTCTCCAGGCTGCCGCTGATAGTTGTTTTAGGGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGcc                     <  1:267708/140‑1 (MQ=255)                                                                                     cgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATTATTAATGTGTTGACTTGcc                     <  2:642695/140‑1 (MQ=255)                                                                                               cAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGCCATATTAATGGc          <  2:477622/140‑1 (MQ=255)                                                                                                      ccgccgATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCg   >  1:156309/1‑140 (MQ=255)                                                                                                       cgccgATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGCCATATTAATGGCAGAGACgg  >  1:190273/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                TCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGA‑TATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGG  >  NC_000913/1593993‑1594233

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: ‑