Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,080,915	(G)5→6	intergenic (+102/‑441)	putP → / → efeU	proline:sodium symporter/ferrous iron permease (pseudogene)

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,080,910	1	.	G	100.0%	129.0 / NA	39	intergenic (+97/‑446)	putP/efeU	proline:sodium symporter/ferrous iron permease (pseudogene)
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (22/17);  total (22/17)

CTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑GGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGAC  >  NC_000913/1080785‑1081042                                                                                                                               |                                                                                                                                     cTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCa                                                                                                                                       <  1:242118/126‑1 (MQ=255) cTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCa                                                                                                                                       >  2:242118/1‑126 (MQ=255)                             aGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCt                                                                                              >  1:1003960/1‑139 (MQ=255)                               ggACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTc                                                                                            >  2:1197753/1‑139 (MQ=255)                                    tAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGa                                                                                       >  1:1079297/1‑139 (MQ=255)                                           cggcggTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTc                                                                                >  2:1327986/1‑139 (MQ=255)                                                        tgGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACg                                                                   <  1:1327986/139‑1 (MQ=255)                                                             tCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGccacc                                                              <  1:1197753/139‑1 (MQ=255)                                                                       gTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    <  2:1012475/139‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACg                                                                   >  1:1333979/1‑105 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACg                                                                   <  2:1333979/105‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      >  1:1280618/1‑118 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      <  2:1280618/118‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      >  2:622225/1‑118 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      <  1:622225/118‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    >  1:11699/1‑120 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    >  1:1167017/1‑120 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    <  2:11699/120‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    <  2:1167017/120‑1 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGc                                 >  1:1029005/1‑139 (MQ=255)                                                                                          ccTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGc                                 >  2:220141/1‑139 (MQ=255)                                                                                              gCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCt                                                                                              >  1:1366254/1‑74 (MQ=255)                                                                                              gCCATATAAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCt                                                                                              <  2:1366254/74‑1 (MQ=255)                                                                                                    taAATTGAATGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGaa                                                                                      >  2:18399/1‑76 (MQ=255)                                                                                                    taAATTGAATGGGGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGaa                                                                                      <  1:18399/76‑1 (MQ=25)                                                                                                            aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      <  2:107174/100‑1 (MQ=255)                                                                                                            aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCg                                                      >  1:107174/1‑100 (MQ=255)                                                                                                            aTGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATa               >  2:1144249/1‑139 (MQ=255)                                                                                                             tGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    >  1:427379/1‑101 (MQ=255)                                                                                                             tGGTGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    <  2:427379/101‑1 (MQ=255)                                                                                                                tGCAGGGAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATcg           >  1:1031192/1‑139 (MQ=255)                                                                                                                  cAGGGAGCGCGCAGGGGGGCGGCCAATCgccgccgcc                                                                                                               >  1:1433588/1‑37 (MQ=14)                                                                                                                  cAGGGAGCGCGCAGGGGGGCGGCCAATCgccgccgcc                                                                                                               <  2:1433588/37‑1 (MQ=14)                                                                                                                    gggAGCGCGCAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGa       <  1:220141/139‑1 (MQ=255)                                                                                                                         cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGAc  >  1:1147668/1‑139 (MQ=255)                                                                                                                         cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTCCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGa                                                     <  1:576961/88‑1 (MQ=38)                                                                                                                         cgcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTCCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGa                                                     >  2:576961/1‑88 (MQ=37)                                                                                                                          gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGaa                                                                                      <  2:356871/54‑1 (MQ=25)                                                                                                                          gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGaa                                                                                      >  1:356871/1‑54 (MQ=25)                                                                                                                          gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    <  1:925598/88‑1 (MQ=255)                                                                                                                          gcgcAGGGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAg                                                    >  2:925598/1‑88 (MQ=255)                                                                                                                               |                                                                                                                                     CTCCGCCGTCACGGTTGCAGGAAAGCTAAGGGACTTAGCCTGCGGCGGTTTTGTTTGGCTTCAGCAGCGGGTTGCGCTCCCTTAATGTGCCTCGCCATATAAATTGAATGGTGCAGGGAGCGCGCA‑GGGGGCGGCCAATCGCCGCCGCCCCCTGCTGTCCCGGCCTTCGGGGAACGCTTCAGCGATTTTGACGCCACCAACACCCGAGCTGTTATTATGTTCCGGGCAAAAAGTTAGATTTGATAATCGCGGATGGAC  >  NC_000913/1080785‑1081042

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑