Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,428,923	Δ1 bp	intergenic (‑161/‑313)	rrsD ← / → yrdA	16S ribosomal RNA/protein YrdA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,428,923	0	C	.	100.0%	115.0 / NA	34	intergenic (‑161/‑313)	rrsD/yrdA	16S ribosomal RNA/protein YrdA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (15/19);  total (15/19)

TGCCCACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGCGGCTTTCAGCTCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAGG  >  NC_000913/3428870‑3429052                                                      |                                                                                                                                  tGCCCACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCg                                           >  2:1211422/1‑140 (MQ=255)  gCCCACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGa                                          <  2:540981/140‑1 (MQ=255)   cccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAGCCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGa                                          <  1:1023445/139‑1 (MQ=11)   cccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGa                                          >  2:1023445/1‑139 (MQ=255)   cccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAc                                         >  1:515312/1‑140 (MQ=255)    ccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAcc                                        <  1:838312/140‑1 (MQ=255)    ccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAcc                                        <  1:682888/140‑1 (MQ=255)    ccACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAcc                                        <  2:816852/140‑1 (MQ=255)        acaGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAcc                                        <  1:340507/136‑1 (MQ=255)        acaGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGAcc                                        >  2:340507/1‑136 (MQ=255)            aTTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCtgtg                                >  1:304068/1‑140 (MQ=255)             ttGTCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGa                               <  2:1105352/140‑1 (MQ=255)                tCTGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAgt                            >  2:116058/1‑140 (MQ=255)                  tGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATc                                     <  1:621216/129‑1 (MQ=14)                  tGATAAATTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATc                                     >  2:621216/1‑129 (MQ=11)                      aaaTTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCa                      >  2:681501/1‑140 (MQ=17)                        aTTGTTAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACg                    <  2:515312/140‑1 (MQ=255)                            ttAAAGAGCAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTgt                <  2:1058009/140‑1 (MQ=255)                              aaaGAGCAGTTGCGACGCGCCTT‑‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACg                    <  1:525455/134‑1 (MQ=17)                              aaaGAGCAGTTGCGACGCGCCTT‑‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACg                    >  2:525455/1‑134 (MQ=17)                                    cAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCaa        >  2:649844/1‑140 (MQ=255)                                    cAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCaa        >  2:934381/1‑140 (MQ=18)                                    cAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCaa        >  2:452302/1‑140 (MQ=18)                                    cAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCaa        >  1:387863/1‑140 (MQ=18)                                    cAGTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCaa        <  1:247830/140‑1 (MQ=255)                                      gTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGtt                  <  2:344227/128‑1 (MQ=17)                                      gTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGtt                  >  1:344227/1‑128 (MQ=17)                                      gTTGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACg      >  2:625213/1‑140 (MQ=18)                                       ttGCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACgg     <  1:116058/140‑1 (MQ=255)                                         gCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAg   <  2:387863/140‑1 (MQ=255)                                         gCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAg   <  2:173324/140‑1 (MQ=255)                                         gCGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAg   <  1:452302/140‑1 (MQ=255)                                          cGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAgg  <  1:625213/140‑1 (MQ=255)                                          cGACGC‑GCTTT‑AGCGCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAgg  <  2:809434/140‑1 (MQ=255)                                                      |                                                                                                                                  TGCCCACACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGACGCGGCTTTCAGCTCACTGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTTCAGAGTCAACCCTGAATTTCAGGATTTTTTTCTCTTCGTTGTTCCGACCATCCTGTGAAGTGTTTCACGTTGTCGTCTCAACGGAGG  >  NC_000913/3428870‑3429052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑