Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_017635	3,127,359	C→T	pseudogene (675/1425 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	3,127,359	0	C	T	75.0%	10.4 / 4.3	12	pseudogene (675/1425 nt)	tssA	type VI secretion system protein TssA
Reads supporting (aligned to +/- strand):  ref base C (2/1);  new base T (6/3);  total (8/4)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.11e-01

TGTGGACGGCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAACTGCTG  >  NC_017635/3127311‑3127404                                                 |                                              tgtgGCCGCAAAATCCGGGCGGGCCCCGCCGCGCACCGAGTCACGCAAcc                                              <  2:292293/50‑1 (MQ=9)  gtgGACGGAAAACCCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAAcc                                              <  2:1383937/49‑1 (MQ=14)        ggCAAAACCCGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCtt                                         >  1:1354080/1‑48 (MQ=11)        ggCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCtt                                         >  1:1641102/1‑48 (MQ=255)          cAAACCCCGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGc                                     <  2:660221/50‑1 (MQ=11)                ccGGCTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGt                               <  1:1861157/50‑1 (MQ=11)                  ggCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTAt                             >  2:1977218/1‑50 (MQ=255)                    cTGGTCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGTATGc                           >  1:1446135/1‑50 (MQ=11)                    cTGGCCCCGCCGCGCACCGAGTCACGCAATCAGCTTAAGCGGCTGTATGc                           <  2:794644/50‑1 (MQ=255)                      ggCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGcgc                         <  2:633960/50‑3 (MQ=17)                                      gAGTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACgg          >  2:1478887/1‑49 (MQ=255)                                        gTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAAc       >  2:1563272/1‑50 (MQ=255)                                        gTCACGCAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAAc       >  2:569208/1‑50 (MQ=255)                                              cAATCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAActgctg  >  2:1526738/1‑49 (MQ=255)                                                 |                                              TGTGGACGGCAAAACCCGGCTGGCCCCGCCGCGCACCGAGTCACGCAACCAGCTTAAGCGGCTGTATGCCCAGCAGAACTGGACGGAACTGCTG  >  NC_017635/3127311‑3127404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑