Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	663,410	0	G	T	42.9%	19.1 / 13.7	14	I348I (ATC→ATA)	ECW_RS03175	type VI secretion system tip protein VgrG
Reads supporting (aligned to +/- strand):  ref base G (2/6);  new base T (1/5);  total (3/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as consensus: Frequency below/above cutoff threshold.

CCAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGATCACCGCAAAATGGTTCTCCAGCGCCGTCCCCGCTCCCTGCCGTCC  >  NC_017635/663364‑663457                                               |                                                ccAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGTAtt                                              <  2:680616/50‑2 (MQ=255) ccAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGAt                                               >  1:263351/1‑49 (MQ=255) ccAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGATc                                              <  1:1879002/50‑1 (MQ=255)  cAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGTAtta                                             <  1:66723/50‑3 (MQ=14)  cAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGTAtta                                             <  2:512814/50‑3 (MQ=14)    gCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGATCAcc                                           <  1:1541934/50‑1 (MQ=255)    gCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGATCAcc                                           <  1:646507/50‑1 (MQ=255)     cGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGTATTACCg                                          <  2:1057486/50‑1 (MQ=11)            aGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGTATTACCGCAAAATg                                   <  2:819513/50‑1 (MQ=14)                       tgGTCGCCATGTTCTGTCTGCCGGTATTACCGCAAAATGGTTATCCAgcg                        >  2:1783931/1‑50 (MQ=11)                            gCCATGTTCTGGCTGCCGGGATCACCGCAAAATGGTTCTCCAGCGCCGt                    <  2:2015575/49‑1 (MQ=255)                               aTGTTCTGTCTGCCGGGATCACCGCAAAATGGTTCTCCAGCGCCGTcccg                <  1:1433417/50‑2 (MQ=255)                                 gTTCTGTCTGCCGGGATCACCGCAAAATGGTTCTCCAGCGCCGTCCCCGc              >  1:990676/1‑50 (MQ=255)                                           ccGGGATCACCGCAAAATGGTTCTCCAGCGCCGTCCCCGCTCCCTGCCGt    <  1:925704/50‑1 (MQ=255)                                             gggATCACCGCAAAATGGTTCTCCAGCGCCGTCCCCGCTCCCTGCCGTcc  >  1:1617418/1‑50 (MQ=255)                                               |                                                CCAGCGGTTTCAGCAACGGCTGTGGTCGCCATGTTCTGTCTGCCGGGATCACCGCAAAATGGTTCTCCAGCGCCGTCCCCGCTCCCTGCCGTCC  >  NC_017635/663364‑663457

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: ‑