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%	331.7 / NA	66	intergenic (+89/‑6)	yggI/endA	conserved protein YggI/DNA‑specific endonuclease I
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (30/36);  total (30/36)

ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385                                              |                                             aCCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         >  1:151187/1‑50 (MQ=255)  ccAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTg                                         <  1:5481585/49‑1 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       <  1:6384705‑M1/50‑3 (MQ=255)   cAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:2718075‑M1/1‑48 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcct                                      <  1:2582621‑M1/50‑4 (MQ=255)    aaaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcc                                       >  1:1478872‑M1/1‑47 (MQ=255)     aaaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:2247793‑M1/1‑46 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctac                                    <  1:72213‑M1/50‑6 (MQ=255)      aaCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGccta                                     >  1:4621518‑M1/1‑45 (MQ=255)       aCAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctaca                                   >  1:368153‑M1/1‑44 (MQ=255)        cAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacac                                  <  1:371760‑M1/50‑8 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:5307656‑M1/50‑11 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               >  1:367004‑M1/1‑40 (MQ=255)           cTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactag                               <  1:3226151‑M1/50‑11 (MQ=255)            tttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              >  1:988490‑M1/1‑39 (MQ=255)             ttCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcg                             >  1:1608145‑M1/1‑38 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgg                            >  1:5841049‑M1/1‑37 (MQ=255)              tCGCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagc                              <  1:2225764‑M1/48‑12 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:5396952‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          <  1:276596‑M1/50‑16 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:6674222‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:5288187‑M1/1‑35 (MQ=255)                gCTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcggga                          >  1:3126868‑M1/1‑35 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         <  1:3890414‑M1/50‑17 (MQ=255)                 cTACGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggat                         >  1:2612779‑M1/1‑34 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattct                      <  1:2472859‑M1/50‑20 (MQ=255)                    cGTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggatt                        <  1:2984731‑M1/48‑18 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:3861337‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:1513341‑M1/50‑21 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:2109458‑M1/1‑30 (MQ=255)                     gTTGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     <  1:1677434‑M1/50‑21 (MQ=255)                     gTTCCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctt                     >  1:583392‑M1/1‑30 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    <  1:4346097‑M1/50‑22 (MQ=255)                      ttGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttt                    <  1:2590883‑M1/50‑22 (MQ=255)                       tGCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattccttt                   >  1:5368968‑M1/1‑28 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  >  1:2204273‑M1/1‑27 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  >  1:2566126‑M1/1‑27 (MQ=255)                        gCTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttt                   <  1:2002121‑M1/49‑23 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:5415509‑M1/50‑25 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttg                 <  1:1162851‑M1/50‑25 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:6323256‑M1/49‑24 (MQ=255)                         cTGGCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattcttttt                  <  1:1034210‑M1/49‑24 (MQ=255)                           ggCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgt                >  1:5123201‑M1/1‑24 (MQ=255)                            gCTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgtt               <  1:4360135‑M1/49‑27 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:811854‑M1/50‑29 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             >  1:2840513‑M1/1‑22 (MQ=255)                             cTCGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaa             <  1:319028‑M1/50‑29 (MQ=255)                               cGTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           >  1:73884‑M1/1‑20 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:4497297‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:664059‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          <  1:5555835‑M1/50‑32 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccc          >  1:1636462‑M1/1‑19 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacc           <  1:2194355‑M1/49‑31 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:3059789‑M1/48‑30 (MQ=255)                                gTTTTAACACGGAG‑AAGTGcctacactagcgggattctttttgttaac            <  1:6508837‑M1/48‑30 (MQ=255)                                 ttttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccc         >  1:1038782‑M1/1‑18 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaaccccta       >  1:4092360‑M1/1‑16 (MQ=255)                                   ttAACACGGAG‑AAGTGcctacactagcgggattctttttgttaacccct        <  1:3553850‑M1/49‑34 (MQ=255)                                   ttAACACGGAG‑AAATGcctacactagcgggattctttttgttaacccct        <  1:4009270‑M1/49‑34 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:1750864‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:3586039‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:1377266‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:5141613‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctaccc    <  1:429381‑M1/50‑38 (MQ=255)                                      acacGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacc     <  1:5286955‑M1/49‑37 (MQ=255)                                        acGGAG‑AAGTGcctacactagcgggattctttttgttaacccctacccca  >  1:3206179‑M1/1‑11 (MQ=255)                                              |                                             ACCAAAACAGCTTTCGCTACGTTGCTGGCTCGTTTTAACACGGAGTAAGTGATGTACCGTTATTTGTCTATTGCTGCGGTGGTACTGAGC  >  NC_000913/3090296‑3090385

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑