Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,773,549	T→C	S78P (TCT→CCT)	yfjW →	CP4‑57 prophage; uncharacterized protein YfjW

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,773,549	0	T	C	92.3%	32.9 / ‑3.4	13	S78P (TCT→CCT)	yfjW	CP4‑57 prophage; uncharacterized protein YfjW
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (4/8);  total (4/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.50e-01

GTTATGAATGCTCAATGAAACTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATATCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACATTATTAGCTATTA  >  NC_000913/2773475‑2773624                                                                           |                                                                            gTTATGAATGCTCAATGAAACTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATATctgct                                                                        <  1:499543/80‑1 (MQ=255)  ttATGAATGCTCAATGAAACTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATACCTGCTGt                                                                      <  1:499544/81‑1 (MQ=255)        aTGCTCAATGAAACTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATACCTGCTGTTGCAGt                                                                <  1:499545/81‑1 (MQ=255)                     cTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCt                                                   <  2:499546/81‑1 (MQ=255)                                 aaaCAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAg                                       >  2:499561/1‑81 (MQ=255)                                      attttattttTCACTGGAAACCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAg                                  <  2:499547/81‑1 (MQ=255)                                                     ggAAACCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTAtt                    >  2:499562/1‑80 (MQ=255)                                                      gAAACCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTAttt                   <  2:499548/80‑1 (MQ=255)                                                        aaCCGCATGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAAc                <  2:499549/81‑1 (MQ=255)                                                              aTGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACattat           >  2:499560/1‑80 (MQ=255)                                                               tGGTACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACattat           >  2:499563/1‑79 (MQ=255)                                                                  tACCTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACATTATTAGCt      <  2:499550/81‑1 (MQ=255)                                                                     cTCATACCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACATTATTAGCTAtt   <  2:499551/81‑1 (MQ=255)                                                                        atacCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACATTATTAGCTATTa  <  1:499552/79‑1 (MQ=255)                                                                           |                                                                            GTTATGAATGCTCAATGAAACTTGATTACATAAAACAATTTTATTTTTCACTGGAAACCGCATGGTACCTCATATCTGCTGTTGCAGTATTTATTGCATCTGTTTTTATACAGCATAGAATTAAAGCTTATTTAACATTATTAGCTATTA  >  NC_000913/2773475‑2773624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑