Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,634,151	Δ1 bp	coding (164/534 nt)	rrrQ ←	lysozyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,634,150	0	G	.	93.1%	105.5 / 3.9	29	coding (165/534 nt)	rrrQ	lysozyme
Reads supporting (aligned to +/- strand):  ref base G (0/2);  new base . (7/20);  total (7/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.91e-01

TCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAA  >  NZ_CP009273/1634067‑1634235                                                                                    |                                                                                      tCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCAccc                                                                                 <  1:170016/90‑1 (MQ=255)        cAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAt                                                                         <  2:688993/90‑1 (MQ=255)        cAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGAt                                                                         <  1:772705/90‑1 (MQ=255)          aTGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATgg                                                                       >  2:346182/1‑90 (MQ=255)           tGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATgg                                                                       <  1:211278/90‑1 (MQ=255)               gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                                  >  2:630646/1‑90 (MQ=255)               gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                                  <  1:549675/90‑1 (MQ=255)               gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                                  <  1:630646/90‑1 (MQ=255)               gTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCat                                                                  <  1:56596/90‑1 (MQ=255)                ttGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCata                                                                 <  1:117305/90‑1 (MQ=255)                ttGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCata                                                                 <  2:87604/90‑1 (MQ=255)                       ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa                                                          >  1:556918/1‑90 (MQ=255)                       ggTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGa                                                          >  2:779353/1‑90 (MQ=255)                            cATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCAt                                                     >  1:265736/1‑90 (MQ=255)                             aTTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATc                                                    <  1:100022/90‑1 (MQ=255)                             aTTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATc                                                    <  2:793589/90‑1 (MQ=255)                               ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc                                                  <  2:72468/90‑1 (MQ=255)                               ttttCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc                                                  <  1:799877/90‑1 (MQ=255)                               ttttCCTTCGACAGTTCCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATcgc                                                  <  2:41890/90‑1 (MQ=255)                                      tCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGc                                           >  2:597525/1‑90 (MQ=255)                                         aCAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCAt                                        <  1:290350/90‑1 (MQ=255)                                                              cGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTc                   <  2:64031/90‑1 (MQ=255)                                                              cGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTc                   <  1:196671/90‑1 (MQ=255)                                                              cGGTTTTTCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTc                   <  2:69292/90‑1 (MQ=255)                                                                 tttttCCATCCACCACTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTc                >  1:254794/1‑90 (MQ=255)                                                                        atccgCCTCTGT‑GCACCCGGACAGATGGTCCCTATGCCAGAAGCATCGCGGTATGCCATTGTGTGGTTGCCTTCTTTTTCGTCCAGAAAc         <  2:539020/90‑1 (MQ=255)                                                                             ccacTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTc    <  1:61692/90‑1 (MQ=255)                                                                               acTGT‑GCACCCCGCCAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCaa  <  2:829948/90‑1 (MQ=255)                                                                               acTGT‑GCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCaa  <  2:142287/90‑1 (MQ=255)                                                                                    |                                                                                      TCACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAA  >  NZ_CP009273/1634067‑1634235

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑