Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,090,341	Δ1 bp	intergenic (+89/‑6)	yggI → / → endA	conserved protein YggI/DNA‑specific endonuclease I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,090,341	0	T	.	100.0%	267.2 / NA	54	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (26/28);  total (26/28)

CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090297‑3090385                                             |                                             ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:324401/49‑1 (MQ=255) ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:1384849/49‑1 (MQ=255) ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGc                                        >  1:5008048‑M1/1‑49 (MQ=255)  cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       <  1:2970233‑M1/50‑3 (MQ=255)   aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                      <  1:2612521‑M1/50‑4 (MQ=255)    aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:3610763‑M1/1‑46 (MQ=255)     aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:422601‑M1/50‑6 (MQ=255)      aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:4356648‑M1/1‑44 (MQ=255)       cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:1537157‑M1/50‑8 (MQ=255)       cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:2152872‑M1/1‑43 (MQ=255)       cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:3334401‑M1/50‑8 (MQ=255)        aGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacact                                 <  1:3796175‑M1/50‑9 (MQ=255)         gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacacta                                <  1:3305867‑M1/50‑10 (MQ=255)         gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:2909583‑M1/1‑41 (MQ=255)         gCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  >  1:4033932‑M1/1‑41 (MQ=255)          cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:4500794‑M1/50‑11 (MQ=255)           tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:1262011‑M1/1‑39 (MQ=255)            ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:1076187‑M1/1‑38 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:4073437‑M1/48‑12 (MQ=255)             tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:1492384‑M1/48‑12 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:2692300‑M1/1‑35 (MQ=255)               gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:2299310‑M1/1‑35 (MQ=255)                  aCGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattc                       >  1:4075160‑M1/1‑32 (MQ=255)                   cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:883328‑M1/50‑20 (MQ=255)                    gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatcctt                     <  1:4894664‑M1/50‑21 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacgctagcgggattcttt                    <  1:279609‑M1/50‑22 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    >  1:4354384‑M1/1‑29 (MQ=255)                     ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    >  1:756134‑M1/1‑29 (MQ=255)                      tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   >  1:3865850‑M1/1‑28 (MQ=255)                       gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggcttcttttt                  >  1:3924787‑M1/1‑27 (MQ=255)                       gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  >  1:4586189‑M1/1‑27 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:2984585‑M1/50‑25 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:1507467‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:3480079‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:2416556‑M1/49‑24 (MQ=255)                        cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:1631644‑M1/49‑24 (MQ=255)                         tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:4359424‑M1/1‑25 (MQ=255)                         tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:1996348‑M1/1‑25 (MQ=255)                         tGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:3312182‑M1/1‑25 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtta              <  1:4912046‑M1/50‑28 (MQ=255)                           gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:4867406‑M1/49‑27 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:308653‑M1/1‑22 (MQ=255)                            cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:786069‑M1/50‑29 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:5115743‑M1/50‑32 (MQ=255)                               gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:2259857‑M1/50‑32 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:4933322‑M1/1‑17 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:3100911‑M1/1‑17 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:1029261‑M1/1‑17 (MQ=255)                                 tttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:283541‑M1/1‑17 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       >  1:2686440‑M1/1‑16 (MQ=255)                                  ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:4095777‑M1/49‑34 (MQ=255)                                      cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:4302130‑M1/50‑39 (MQ=255)                                      cacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccc   <  1:2503857‑M1/50‑39 (MQ=255)                                       acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:1687486‑M1/1‑11 (MQ=255)                                             |                                             CCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090297‑3090385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑