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	96.0%	85.2 / ‑3.8	25	pseudogene (2/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (15/9);  total (15/10)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATAT  >  NC_000913/1593985‑1594263                                                                                                                                             |                                                                                                                                             gAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑cccc‑ccccca                                                                                                                                   <  2:584625/150‑3 (MQ=255)                  tctttCCGGTATATTTGCCGTTAACGGTCAGTACTTTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCTTTCCGCCATTCTCCAGGTTCCCGCCCTTATTGGGTTTAGGGACCCGCAGTG‑CCCCACCCCAGGCATAACGTTCata                                                                                                                     <  1:6173/146‑1 (MQ=255)                    tttCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCAcc                                                                                                                >  2:4726/1‑151 (MQ=255)                         ggTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGc                                                                                                             >  2:478350/1‑149 (MQ=255)                          gTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgt                                                                                                          >  1:45235/1‑151 (MQ=255)                          gTATAGTGGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGTTTGCCGCCGATAGTGGTTTTAGCGGCACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCa                                                                                                            <  2:184791/149‑1 (MQ=255)                              aGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAgtggt                                                                                                       <  1:498874/150‑1 (MQ=255)                                        aaCGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCg                                                                                            >  2:107005/1‑151 (MQ=255)                                           ggTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                                                                     <  1:344459/139‑1 (MQ=255)                                           ggTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGa                                                                                                     >  2:344462/1‑139 (MQ=255)                                               aGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATcac                                                                                     >  2:661230/1‑151 (MQ=255)                                                 tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                                   >  2:534700/1‑151 (MQ=255)                                                   cATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTTGTGACATTTCCCGACATCACAcc                                                                                  <  1:599062/150‑1 (MQ=255)                                                    aTTCCCCGGTTTCCCCCCTTCGCTATTCTTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGc                                                                                >  1:479711/1‑151 (MQ=255)                                                       ccccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg                                                                              <  2:204523/150‑1 (MQ=255)                                                        cccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                            <  2:602372/151‑1 (MQ=255)                                                                ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGatat                                                                    >  2:250412/1‑151 (MQ=255)                                                                ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGatat                                                                    <  1:317762/151‑1 (MQ=255)                                                                              tCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACtt                                                      >  1:600501/1‑151 (MQ=255)                                                                                aTTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGc                                                    <  2:64918/151‑1 (MQ=255)                                                                                    gAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                                 >  2:327427/1‑150 (MQ=255)                                                                                       ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATAtt                                              >  2:490391/1‑150 (MQ=255)                                                                                                   tctcCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCg                                 >  1:550319/1‑151 (MQ=255)                                                                                                             gccgccGATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAg                       <  2:131529/151‑1 (MQ=255)                                                                                                                  cgATAGTGGTTTTAGCGACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAAtt                  >  1:542617/1‑151 (MQ=255)                                                                                                                                  gACACGCAGTGCCCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGatat  >  2:589809/1‑151 (MQ=255)                                                                                                                                             |                                                                                                                                             GAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCC‑CCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCACGATAT  >  NC_000913/1593985‑1594263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑