Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,223,868	C→A	pseudogene (305/344 nt)	ycgI →	protein YcgI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,223,868	0	C	A	100.0%	107.1 / NA	32	pseudogene (305/344 nt)	ycgI	protein YcgI
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (19/13);  total (19/13)

AATGACGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCCCCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCGCCAGTTACGGCGGG  >  NC_000913/1223737‑1224003                                                                                                                                    |                                                                                                                                        aatGACGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGaa                                                                                                                                 <  2:240950/140‑1 (MQ=255)   tGACGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAAcg                                                                                                                               >  2:167741/1‑140 (MQ=255)     aCGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAAcgcg                                                                                                                             >  2:60275/1‑140 (MQ=255)     aCGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAAcgcg                                                                                                                             >  1:384285/1‑140 (MQ=255)        gTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTg                                                                                                                          >  2:502294/1‑140 (MQ=255)        gTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTg                                                                                                                          >  2:455968/1‑140 (MQ=255)         tAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTgg                                                                                                                         <  2:190968/140‑1 (MQ=255)              tCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGgt                                                                                                                    <  2:20330/140‑1 (MQ=255)                   aaTGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGaa                                                                                                               <  2:73872/140‑1 (MQ=255)                   aaTGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGaa                                                                                                               <  2:434019/140‑1 (MQ=255)                    aTGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAAc                                                                                                              <  2:277004/140‑1 (MQ=255)                      gATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTg                                                                                                            <  2:237401/140‑1 (MQ=255)                               ggCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTg                                                                                                   >  1:229552/1‑140 (MQ=255)                                     cGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATc                                                                                             <  1:28944/140‑1 (MQ=255)                                      gTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCa                                                                                            <  2:384285/140‑1 (MQ=255)                                      gTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCa                                                                                            >  1:477225/1‑140 (MQ=255)                                                        cTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTc                                                                          >  1:193587/1‑140 (MQ=255)                                                                     aTTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCg                                                             >  2:361733/1‑140 (MQ=255)                                                                     aTTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGCGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCg                                                             >  2:109244/1‑140 (MQ=255)                                                                           cagTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACa                                                       <  1:176617/140‑1 (MQ=255)                                                                              tACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGa                                                    <  2:353560/140‑1 (MQ=255)                                                                              tACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGa                                                    >  1:26631/1‑140 (MQ=255)                                                                               aCGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGAt                                                   >  2:27314/1‑140 (MQ=255)                                                                                cGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATg                                                  >  2:41926/1‑140 (MQ=255)                                                                                                    gtggggtATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTggg                              <  2:222784/140‑1 (MQ=255)                                                                                                        ggtATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCaa                          >  2:411452/1‑140 (MQ=255)                                                                                                        ggtATAGCCATGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCaa                          >  1:509386/1‑140 (MQ=255)                                                                                                                  tGGTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCg                >  2:368677/1‑140 (MQ=255)                                                                                                                   ggTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCGc               >  1:345402/1‑140 (MQ=255)                                                                                                                    gTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCGcc              >  1:40219/1‑140 (MQ=255)                                                                                                                    gTGCCGGTGTGGAATCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCGcc              >  2:79195/1‑140 (MQ=255)                                                                                                                                aaTCACCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGCGCAAAAAAAGCCCGCCAGTTACGGCggg  <  2:468337/140‑1 (MQ=255)                                                                                                                                    |                                                                                                                                        AATGACGGTAATTTCGTCAATGATTTGTCGGGCAGACGTGGAATATACCAGGCAGCTATTAAAGCCTCATTCAGCAGTACGTTTAGCGGACATCTCGGGGTGGGGTATAGCCATGGTGCCGGTGTGGAATCCCCGTGGAACGCGGTGGCTGGTGTGAACTGGTCGTTCTGACCATCAACGATTAAACTGCGCTTCGGCGCAGTTTTCGTTTACAGGATGTTGAAAGGGAAAATTCTGGGGCAAAAAAAGCCCGCCAGTTACGGCGGG  >  NC_000913/1223737‑1224003

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑