Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,127,431	C→T	pseudogene (747/1425 nt)	tssA →	type VI secretion system protein TssA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_017635	3,127,431	0	C	T	100.0%	10.6 / NA	8	pseudogene (747/1425 nt)	tssA	type VI secretion system protein TssA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (4/4);  total (4/4)

AGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGG  >  NC_017635/3127406‑3127477                          |                                               aGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGAc                        <  1:57796/50‑1 (MQ=12)   cAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGCCTGGACAt                      >  1:2043104/1‑50 (MQ=11)    aGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAtt                     >  1:1401216/1‑49 (MQ=255)     ggCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAttc                    <  2:658572/50‑3 (MQ=11)      gCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAtt                     >  2:1773650/1‑47 (MQ=255)               aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATc           <  1:199993/49‑1 (MQ=11)               aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCt          <  2:1148457/50‑1 (MQ=11)                       cACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAgg  >  2:1773599/1‑50 (MQ=11)                          |                                               AGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGG  >  NC_017635/3127406‑3127477

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑