Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,450,720	T→C	S329P (TCC→CCC)	gspD →	type II secretion system secretin GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,450,720	0	T	C	100.0%	68.8 / NA	20	S329P (TCC→CCC)	gspD	type II secretion system secretin GspD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/9);  total (11/9)

CCTCCTCTTCTGGCGCGATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGT  >  NZ_CP009273/3450640‑3450805                                                                                 |                                                                                      cctcctCTTCTGGCGCGATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAgg                                                                              >  2:171602/1‑90 (MQ=255)   tcctcTTCTGGCGCGATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGaa                                                                            >  1:210182/1‑90 (MQ=255)    cctcTTCTGGCGCGATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGaaa                                                                           >  1:516827/1‑90 (MQ=255)               gcgATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACg                                                                >  1:458339/1‑90 (MQ=255)                 gATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGt                                                              >  2:408924/1‑90 (MQ=255)                       tAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTgc                                                        <  1:171602/90‑1 (MQ=255)                             cccaaTTCCCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCt                                                  <  1:421608/86‑1 (MQ=255)                                       gccgATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGc                                        <  1:117719/90‑1 (MQ=255)                                              aaCAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGcac                                 <  2:508568/90‑1 (MQ=255)                                               aCAGACTAACTCTCTGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGcaca                                <  1:442323/90‑1 (MQ=255)                                                          ctctGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTg                     >  1:215036/1‑90 (MQ=255)                                                            ctGGTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAg                   >  1:81069/1‑90 (MQ=255)                                                              ggTCATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGc                 >  1:385314/1‑90 (MQ=255)                                                                 cATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTg                     >  2:341412/1‑83 (MQ=255)                                                                 cATTACCGCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTg                     <  1:341412/83‑1 (MQ=255)                                                                        gCTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGtt       >  2:275957/1‑90 (MQ=255)                                                                         cTGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTg      <  2:385314/90‑1 (MQ=255)                                                                          tGACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGa     <  2:168520/90‑1 (MQ=255)                                                                           gACCAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGaa    >  2:126156/1‑90 (MQ=255)                                                                             ccAGCCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGt  <  2:234139/90‑1 (MQ=255)                                                                                 |                                                                                      CCTCCTCTTCTGGCGCGATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGT  >  NZ_CP009273/3450640‑3450805

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑