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	100.0%	104.3 / NA	28	pseudogene (2/1461 nt)	yneO	pseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (14/14);  total (14/14)

ATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCA  >  NC_000913/1594000‑1594257                                                                                                                              |                                                                                                                                       aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCa                                                                                                                          <  1:188591/139‑1 (MQ=255)  ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCGGTG‑‑cccccccccacgcca                                                                                                                        >  2:202973/1‑132 (MQ=255)  ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt                                                                                                                         >  1:482423/1‑139 (MQ=255)  ttGTTTCCGGTATAGTTGCCGGTTACCGTCAGGTCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCAt                                                                                                                         <  2:97532/139‑1 (MQ=255)   tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                        <  2:479983/139‑1 (MQ=255)                              tCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑ccc                                                                                                                                    >  1:223895/1‑99 (MQ=255)                              tCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑ccc                                                                                                                                    <  2:223895/99‑1 (MQ=255)                                  tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTc                                                                                         >  2:397547/1‑139 (MQ=255)                                   aCATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                        <  2:497577/139‑1 (MQ=255)                                       tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑cc                                                                                                                                     <  1:104023/89‑1 (MQ=255)                                       tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑cc                                                                                                                                     >  2:104023/1‑89 (MQ=255)                                          ccGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATc                                                                                 >  1:155588/1‑139 (MQ=255)                                            ggcttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTGCCCGACATcac                                                                               >  2:324230/4‑139 (MQ=255)                                              tttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                             >  1:180311/1‑139 (MQ=255)                                                   ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg                                                                        <  2:180311/139‑1 (MQ=255)                                                   ccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTg                                                                        >  1:443943/1‑139 (MQ=255)                                                      cTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTa                                                                     <  2:301164/139‑1 (MQ=255)                                                       ttCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTa                                                                     >  2:117709/1‑139 (MQ=255)                                                       ttCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                    <  2:486041/139‑1 (MQ=255)                                                                      aaCCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAGTGTGtt                                                     >  2:121186/1‑139 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                        >  1:299745/1‑70 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATa                                                                                                                        <  2:299745/70‑1 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                        <  2:247313/102‑1 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                        >  1:247313/1‑102 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                        <  2:356271/102‑1 (MQ=255)                                                                        ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                        >  1:356271/1‑102 (MQ=255)                                                                          gTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACt                                                 <  2:443943/139‑1 (MQ=255)                                                                           tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACtt                                                >  2:149861/1‑139 (MQ=255)                                                                           tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑ccccccccc                                                                                                                              <  2:343753/60‑2 (MQ=255)                                                                           tGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑ccccccccc                                                                                                                              >  1:343753/1‑59 (MQ=255)                                                                                               ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCGGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                           >  2:245281/1‑92 (MQ=255)                                                                                               ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCGGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                           <  1:245281/92‑1 (MQ=255)                                                                                               ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                           <  2:215013/124‑1 (MQ=255)                                                                                               ccgccgATAGTGGTTTTAGCGACACGCAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                           >  1:215013/1‑124 (MQ=255)                                                                                                                         cAGTGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccccccccc  <  2:232757/139‑2 (MQ=255)                                                                                                                              |                                                                                                                                       ATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCA  >  NC_000913/1594000‑1594257

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑