Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,632,327	T→C	intergenic (‑42/‑563)	ydfJ ← / → ynfT	putative transporter YdfJ/Qin prophage; protein YnfT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,632,327	0	T	C	100.0%	132.7 / NA	39	intergenic (‑42/‑563)	ydfJ/ynfT	putative transporter YdfJ/Qin prophage; protein YnfT
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (18/21);  total (18/21)

GCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCAT  >  NC_000913/1632194‑1632459                                                                                                                                      |                                                                                                                                     gCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTc                                                                                                                                  <  1:694726/138‑1 (MQ=255) gCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTc                                                                                                                                  >  2:694726/1‑138 (MQ=255) gCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTa                                                                                                                                >  2:135766/1‑140 (MQ=255)  ccAGAATTAATGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAg                                                                                                                               <  1:150348/140‑1 (MQ=255)   cAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAgg                                                                                                                              >  2:341279/1‑140 (MQ=255)   cAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAgg                                                                                                                              <  2:237510/140‑1 (MQ=255)          aaCGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTc                                                                                                                       >  2:49591/1‑140 (MQ=255)                 ttGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAgg                                                                                                                              >  2:234594/1‑126 (MQ=255)                 ttGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAgg                                                                                                                              <  1:234594/126‑1 (MQ=255)                 ttGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGt                                                                                                                >  1:567692/1‑140 (MQ=255)                                cacgAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAACCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTaaaa                                                                                                 <  2:408745/137‑1 (MQ=255)                                  ggAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAg                                                                                               <  2:192316/140‑1 (MQ=255)                                         atatTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTa                                                                                        <  1:278495/140‑1 (MQ=255)                                             ttCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGtt                                                                                    <  2:567692/140‑1 (MQ=255)                                                   aaaCACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGAtct                                                                              <  1:248042/140‑1 (MQ=255)                                                   aaaCACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGAtct                                                                              <  1:221499/140‑1 (MQ=255)                                                        cTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAgtg                                                                         <  2:825661/140‑1 (MQ=255)                                                              cTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATc                                                                   >  2:266010/1‑140 (MQ=255)                                                                gcgcCGAGCGAATATAACTGGAAATTCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTg                                                                 >  1:827239/1‑140 (MQ=255)                                                                 cgcCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTgg                                                                >  2:481732/1‑140 (MQ=255)                                                                     gAGCGAATATAACTGGAAATTCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGcc                                                            <  2:827239/140‑1 (MQ=255)                                                                     gAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGcc                                                            <  2:382254/140‑1 (MQ=255)                                                                          aaTATAACTGGAAATCCATAATTCACAGTTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTAttt                                                       <  1:152214/140‑1 (MQ=255)                                                                            tataACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCt                                                     <  1:49591/140‑1 (MQ=255)                                                                            tataACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCt                                                     <  1:481732/140‑1 (MQ=255)                                                                              taACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGt                                                   <  1:341279/140‑1 (MQ=255)                                                                               aaCTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTc                                                  <  2:502771/140‑1 (MQ=255)                                                                                       aTCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCatatat                                          >  2:115596/1‑140 (MQ=255)                                                                                            tAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGcccc                                     >  2:121235/1‑140 (MQ=255)                                                                                            tAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGcccc                                     >  1:498097/1‑140 (MQ=255)                                                                                                  acaGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCaaaaaa                               >  1:121326/1‑140 (MQ=255)                                                                                                         ttttttCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCAGCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTcccc                        >  2:577163/1‑140 (MQ=255)                                                                                                           ttttCCCATCCTGTGGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCaa                      <  1:757963/140‑1 (MQ=255)                                                                                                                        tgGTTTCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGtt         >  1:143580/1‑140 (MQ=255)                                                                                                                             tCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGa                  <  1:768115/126‑1 (MQ=255)                                                                                                                             tCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGa                  >  2:768115/1‑126 (MQ=255)                                                                                                                             tCCTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCAGCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTc    <  1:521850/140‑1 (MQ=255)                                                                                                                               cTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCAt  >  2:536792/1‑140 (MQ=255)                                                                                                                               cTTGGCGCTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCAt  >  1:135178/1‑140 (MQ=255)                                                                                                                                      |                                                                                                                                     GCCAGAATTAACGCCATTGCCGTTGATGATTCAGGAAAAAATATTTCATGAAACACTAACGCTGCGCCGAGCGAATATAACTGGAAATCCATAATTCACAGGTGTTTTTTCCCATCCTGTGGTTTCCTTGGCGTTTTCTAGGTTTTTTCAGATAGTTGCATTTTTTTAAAAAGCATCCTAAGTTCGATCTCAGTGTCTATCTGGGGCCTATTTCTGTCCCATATATGCCCCAAAAAAACTCCCCAACAGATAAGTAGTTTTTTCAT  >  NC_000913/1632194‑1632459

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑