Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,209,596	T→C	pseudogene (60/537 nt)	stfE ←	e14 prophage; putative side tail fiber protein fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,209,596	0	T	C	100.0%	71.9 / NA	22	pseudogene (60/537 nt)	stfE	e14 prophage; putative side tail fiber protein fragment
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/11);  total (11/11)

ACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTT  >  NC_000913/1209527‑1209668                                                                      |                                                                         aCCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttc                                                               >  1:239860‑M2/1‑76 (MQ=255)     ttGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcc                                                            <  1:239861‑M2/80‑9 (MQ=255)        cATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaaa                                                        <  1:239884‑M2/81‑13 (MQ=255)        cATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaa                                                         >  2:239862‑M2/1‑69 (MQ=255)            tCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaaaccaa                                                    <  1:239885‑M2/81‑17 (MQ=255)             cagccagcCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaaaccaag                                                   <  1:239863‑M2/81‑18 (MQ=255)             cagccagcCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAAc                                                   >  2:239892/1‑81 (MQ=255)               gccagccTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGt                                                 >  1:239882/1‑81 (MQ=255)                   gccTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTAt                                             >  2:239880/1‑81 (MQ=255)                        ttGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGaaaa                                        <  2:239864/81‑1 (MQ=255)                              gAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaaaccaaggttttcgagagccgttt                                  <  1:1042591‑M2/81‑35 (MQ=255)                                 tGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAAt                               <  1:239865/81‑1 (MQ=255)                                           ccACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCaaa                     >  1:239890/1‑81 (MQ=255)                                            cACGGAACCGGGACACCAACAGGTAACGCAGAGccttctcccaaaccaaggttttcgagagccgtttgcacagtgccatcc                    >  2:239866‑M2/1‑33 (MQ=255)                                            cACGGAACCGGGACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAAt                    >  2:239902/1‑81 (MQ=255)                                                     gggACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCAtt           >  2:239900/1‑81 (MQ=255)                                                       gACACCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTcc         <  2:239867/81‑1 (MQ=255)                                                         cacCAACAGGTAACGCAGAGccttctcccaaaccaaggttttcgagagccgtttgcacagtgccatccgatttgatatcgc       >  1:239868‑M2/1‑20 (MQ=255)                                                         cacCAACAGGTAACGCAGAGccttctcccaaaccaaggttttcgagagccgtttgcacagtgccatccgatttgatatcgc       <  1:239653‑M2/81‑62 (MQ=255)                                                         cacCAACAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTg       >  2:239893/1‑81 (MQ=255)                                                            cAACAGGTAACGCAGAGccttctcccaaaccaaggttttcgagagccgtttgcacagtgccatccgatttgatatcgcca     <  1:239652‑M2/80‑64 (MQ=255)                                                              aCAGGTAACGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCtttt  <  1:239869/81‑1 (MQ=255)                                                                      |                                                                         ACCATTGCATTTCAGCCAGCCTGTTGGCGGAGTGGCTGAAGGCCACGGAACCGGGACACCAACAGGTAATGCAGAGCCTTCTCCCAAACCAACGTTTATGAAAATGAAGAAATAACAAGCAAATGGCATCATTCCTGCTTTT  >  NC_000913/1209527‑1209668

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑