Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,966,502	Δ1 bp	coding (447/1662 nt)	tar ←	methyl‑accepting chemotaxis protein II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,966,500	0	A	.	100.0%	181.6 / NA	42	coding (449/1662 nt)	tar	methyl‑accepting chemotaxis protein II
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (19/23);  total (19/23)

ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT  >  NZ_CP009273/1966413‑1966582                                                                                        |                                                                                   atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                                  >  2:919694/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                                  >  1:267986/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                                  >  2:139691/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                                  >  1:749665/1‑89 (MQ=255)  tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata                                                                                 <  2:921707/90‑3 (MQ=255)  tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata                                                                                 <  2:865893/90‑3 (MQ=255)  tatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaata                                                                                 <  1:987959/90‑3 (MQ=255)        gATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc                                                                          <  1:1200871/90‑1 (MQ=255)         aTACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCa                                                                         >  1:1088049/1‑90 (MQ=255)             aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt                                                                     <  2:1217207/90‑1 (MQ=255)             aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt                                                                     <  2:540279/90‑1 (MQ=255)              gTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAtt                                                                    >  2:942503/1‑90 (MQ=255)                ttttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGc                                                                  >  1:309048/1‑90 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  1:462413/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  2:127693/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  2:32215/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  1:747064/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  2:745679/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATCCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  2:697207/90‑1 (MQ=255)                   tCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCAt                                                               >  1:1110358/1‑90 (MQ=255)                        gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt                                                          >  1:776045/1‑90 (MQ=255)                        gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt                                                          >  2:829692/1‑90 (MQ=255)                        gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt                                                          >  1:220587/1‑90 (MQ=255)                          tgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg                                                        <  1:942503/90‑1 (MQ=255)                               gCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaat                                                   <  2:1088049/90‑1 (MQ=255)                                cGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc                                                                          <  2:1006975/66‑1 (MQ=255)                                cGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTcc                                                                          >  1:1006975/1‑66 (MQ=255)                                  tACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaa                                                >  1:777828/1‑90 (MQ=255)                                    cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                              <  2:292764/90‑1 (MQ=255)                                      gAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcag                                            >  1:962164/1‑90 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                <  1:1212824/68‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                                >  2:1212824/1‑68 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                          <  2:267986/90‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                          >  2:658935/1‑90 (MQ=255)                                             cGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATcagttcagtt                                     <  2:777828/90‑1 (MQ=255)                                                ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc                                  >  1:952257/1‑90 (MQ=255)                                                ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc                                  >  2:736546/1‑90 (MQ=255)                                                  cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                <  2:558158/90‑1 (MQ=255)                                                  cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                <  1:270986/90‑1 (MQ=255)                                                  cGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                <  2:335300/90‑1 (MQ=255)                                                  cGCCCATTGCATTTTCCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                <  2:315672/90‑1 (MQ=255)                                                           cattttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAACCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATa                       <  1:895804/90‑1 (MQ=255)                                                                 gcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                >  1:162147/1‑75 (MQ=255)                                                                 gcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGc                                <  2:162147/75‑1 (MQ=255)                                                                       ccTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATAttt           >  1:1066524/1‑90 (MQ=255)                                                                               ggCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCaa   >  1:411984/1‑90 (MQ=255)                                                                                gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                              <  1:818951/46‑1 (MQ=39)                                                                                gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                              >  2:818951/1‑46 (MQ=39)                                                                                gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAat  >  1:1030024/1‑90 (MQ=255)                                                                                        |                                                                                   ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTTCATCAAT  >  NZ_CP009273/1966413‑1966582

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑