Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	1,202,211	C→T	intergenic (‑127/+48)	ymfJ ← / ← cohE	e14 prophage; uncharacterized protein/e14 prophage; repressor protein phage e14

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	1,202,211	0	C	T	100.0%	142.1 / NA	45	intergenic (‑127/+48)	ymfJ/cohE	e14 prophage; uncharacterized protein/e14 prophage; repressor protein phage e14
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/25);  total (20/25)

TTCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTACATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAGGCCAGTT  >  NC_000913_3_hsa_tpiA/1202065‑1202357                                                                                                                                                   |                                                                                                                                                   ttCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATAtt                                                                                                                                                 <  1:305069/150‑1 (MQ=255)      aTTCTGCTGATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCaa                                                                                                                                            <  2:211091/150‑1 (MQ=255)      aTTCTGCTCATTCATCTATTCTCTCCACTGGAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCaa                                                                                                                                            <  1:600797/150‑1 (MQ=255)       ttCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATTTCAAATGTATATTGTCAAg                                                                                                                                           >  1:42341/1‑150 (MQ=255)             tcattcatCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATaaa                                                                                                                                     >  1:104381/1‑150 (MQ=255)             tcattcatCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATaaa                                                                                                                                     <  1:205282/150‑1 (MQ=255)               attcatCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATaaaaa                                                                                                                                   >  1:637561/1‑150 (MQ=255)                  catCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTGTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAAc                                                                                                                                <  2:479658/150‑1 (MQ=255)                        ttCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGccc                                                                                                                          >  1:83317/1‑149 (MQ=255)                              ccACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAg                                                                                                                    <  1:634814/150‑1 (MQ=255)                               cACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACCTTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTTCCGAAGCAgg                                                                                                                   >  2:680087/1‑150 (MQ=255)                                ccTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGt                                                                                                                  <  1:582447/149‑1 (MQ=255)                                aCTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGcc                                                                                                                           <  1:155283/141‑1 (MQ=255)                                aCTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGcc                                                                                                                           >  2:155283/1‑141 (MQ=255)                                       tcatcCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTATCAAGTATAAAAAAACCTGCCGAAGCACGTTCATaaa                                                                                                           >  2:282905/1‑150 (MQ=255)                                          tcCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACAt                                                                                                        <  2:216241/150‑1 (MQ=255)                                          tcCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACAt                                                                                                        <  2:220252/150‑1 (MQ=255)                                            cGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGtt                                                                                                                 <  1:639900/139‑1 (MQ=255)                                            cGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGtt                                                                                                                 >  2:639900/1‑139 (MQ=255)                                             gCTAACGAATCATCCCGGTCTTCGTACGTACCAAGCGAGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATATATCTCAAAGGTATATTTTCAAGTATAAAAAAACCTGCCGAAGCAGATTCATAAACATTGa                                                                                                     >  2:146789/1‑150 (MQ=255)                                                  ccaaTCATCCCGGTCTTCGTACGGACCGGGGCGGCGACTTCGGGGGGGACCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAgg                                                                                                <  2:628472/148‑1 (MQ=255)                                                             ggTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGGGCGAGGGTCATAAACATTGATTAGGCTTTGATTTTg                                                                                     <  2:675056/150‑1 (MQ=255)                                                                cTTCGTACGTACCGGGCGCGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAt                                                                                  <  1:678982/150‑1 (MQ=255)                                                                 ttCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAtc                                                                                 >  2:55323/1‑150 (MQ=255)                                                                                 gggtTACTGCTTGGGCGTTCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGACGTAGCATGTTCATAAACAGGGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTga                                                                 <  2:148400/150‑1 (MQ=255)                                                                                 gggcTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTga                                                                 >  2:653560/1‑150 (MQ=255)                                                                                  ggcTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTgtg                                                                >  2:68489/1‑148 (MQ=255)                                                                                                  tCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCaa                                                <  2:637561/150‑1 (MQ=255)                                                                                                         tgtttgttGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCAGAAGCAGGTTTTGCAGGATTCGGTAGGTTTTTTTTTTGTATCGCCTTGGTTTTCCTGAGCAAATCATGTTACCAATTATaga                                         <  2:324909/150‑1 (MQ=255)                                                                                                           tttgttGTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGc                                       >  1:423833/1‑150 (MQ=255)                                                                                                            ttgttgTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCa                                      >  1:236767/1‑150 (MQ=255)                                                                                                            ttgttgTTTCTCTTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCa                                      >  1:238811/1‑150 (MQ=255)                                                                                                                       ctTGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGa                           <  1:676406/150‑1 (MQ=255)                                                                                                                        ttGGGTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGAt                          <  2:83317/150‑1 (MQ=255)                                                                                                                           ggTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGtt                             >  2:22554/1‑144 (MQ=255)                                                                                                                           ggTACATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGtt                             <  1:22554/144‑1 (MQ=255)                                                                                                                              aCATTATGTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAAt                    <  1:443756/150‑1 (MQ=255)                                                                                                                                     gTATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATTTAAGGc             >  1:409818/1‑150 (MQ=255)                                                                                                                                      tATCTCAAAGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCt            <  1:55323/150‑1 (MQ=255)                                                                                                                                          taaaaGGTATATTGAAAAGTAGAAAAAAACCTGGCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAgg        <  2:179989/148‑1 (MQ=255)                                                                                                                                           cAAAGGAATATTGTAAAGTATAAAAAAACCTTGCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAGGc       <  2:42341/150‑1 (MQ=255)                                                                                                                                            aaaGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAt                                                                                  >  2:280218/1‑74 (MQ=255)                                                                                                                                            aaaGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTAt                                                                                  <  1:280218/74‑1 (MQ=255)                                                                                                                                            aaaGGTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGTTCTTAATGTAAGGCTCAggac      >  1:119694/1‑148 (MQ=255)                                                                                                                                                gTATATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAGGCCAGtt  >  2:155390/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                   TTCAAATTCTGCTCATTCATCTATTCTCTCCACTGAAATCATCCGCTAACGAATCATCCCGGTCTTCGTACGTACCGGGCGGGCTACTTCGTGGGCGTCCTGCCTGTTTGTTGTTTCTCTTGGGTACATTATGTATCTCAAAGGTACATTGTCAAGTATAAAAAAACCTGCCGAAGCAGGTTCATAAACATTGATTAGGCTTTGATTTTGTATCTTCTTGGTTTTCCTGAGAAAATCACAGTACCAATTATAGAGCAATTACCGTTGATCTTAATGTAAGGCTCAGGCCAGTT  >  NC_000913_3_hsa_tpiA/1202065‑1202357

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑