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%	31.9 / NA	19	pseudogene (747/1425 nt)	tssA	type VI secretion system protein TssA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (3/16);  total (3/16)

CAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCAT  >  NC_017635/3127408‑3127473                        |                                           cAGGCCGACCTGATGTTCAGCTCTGGCGTCAGCCATTTCTGGCTGGAc                    <  1:877298/48‑1 (MQ=11) cAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGAc                    <  2:2447520/48‑1 (MQ=255)  aGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACa                   <  2:220635/48‑1 (MQ=255)      cGACCTGATGTTCAGCACTGGCGTCAGCCAATTCTGGCTGGACATTCa               <  2:1988982/48‑1 (MQ=11)            gATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         >  2:1223024/1‑48 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt          <  1:1071073/46‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGt          <  2:409153/46‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  2:510618/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  2:2548815/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  2:1950593/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  1:399710/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  1:320729/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTa         <  1:1360315/47‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt        <  1:2133545/48‑1 (MQ=11)             aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTAt        <  2:60274/48‑1 (MQ=11)               gTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCt      >  2:1307723/1‑48 (MQ=11)                  cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc    <  2:701923/47‑1 (MQ=11)                  cAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGc    <  1:1308586/47‑1 (MQ=11)                     cACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCAt  >  2:2552346/1‑46 (MQ=11)                        |                                           CAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCAT  >  NC_017635/3127408‑3127473

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑