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	78.6%	30.7 / 4.7	14	pseudogene (3963/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (1/2);  new base C (4/7);  total (5/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGC  >  NC_000913/1593995‑1594225                                                                                                                                    |                                                                                                      aGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑ccc                                                                                                    <  1:269962/133‑1 (MQ=255)    ccATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑cccccc                                                                                                 >  2:457619/1‑133 (MQ=255)              cGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATa                                                                                        <  2:107692/133‑1 (MQ=255)                                cGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCa                                                                      <  1:80133/133‑1 (MQ=255)                                                 ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGa                                                     >  2:85667/1‑133 (MQ=255)                                                 ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGGGGGGACATTTCCCGa                                                     >  1:255795/1‑133 (MQ=255)                                                   tttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTCC‑CCCCCCCCAGGCATAACGTTCTTTTCACCTCCAGCGGTGACATTTCCCGACa                                                   >  2:69805/1‑133 (MQ=255)                                                           cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCTGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                           <  2:295714/133‑1 (MQ=255)                                                              cGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAATGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg                                        <  2:42581/133‑1 (MQ=255)                                                                cTATTCATTTGAACCCTGCCGCCACTCCCCAGTTTGCCGCCAATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                      <  2:148968/133‑1 (MQ=255)                                                                        ttGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGatat                              <  1:457619/133‑1 (MQ=255)                                                                          gAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTCC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTa                            <  1:69805/133‑1 (MQ=255)                                                                           aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTACCGACATGACAGCGGTGTTATTGATATTaa                           >  1:147324/1‑133 (MQ=255)                                                                                         tctcCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc             <  1:85667/133‑1 (MQ=255)                                                                                         tctcCAGGTTCCCGCCGATAGTGGCTTTCGCGCCACGCAGTAC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc             <  2:147324/133‑1 (MQ=255)                                                                                                    ccgccgATAGTGGTTTTAGCGACACGCAGT‑GCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGGTATTAATGTGTTGACTTGCCATATTAATGGc  >  1:512983/1‑133 (MQ=255)                                                                                                                                    |                                                                                                      AGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGT‑G‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGC  >  NC_000913/1593995‑1594225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑