Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,068,276	Δ1 bp	intergenic (+22/+235)	ymdF → / ← rutG	KGG family protein/pyrimidine permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,068,276	0	G	.	100.0%	179.1 / NA	43	intergenic (+22/+235)	ymdF/rutG	KGG family protein/pyrimidine permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (18/25);  total (18/25)

GTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068145‑1068410                                                                                                                                     |                                                                                                                                       gTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTg                                                                                                                                >  1:14960/1‑139 (MQ=255)           tGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGTAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCg                                                                                                                     >  1:598378/1‑139 (MQ=255)           tGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCg                                                                                                                     >  1:248897/1‑139 (MQ=255)                       cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCAt                                                                                                         >  1:601259/1‑139 (MQ=255)                       cGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCAt                                                                                                         >  1:309828/1‑139 (MQ=255)                        gggggTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATc                                                                                                        >  2:708901/1‑139 (MQ=255)                           ggTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCAcc                                                                                                     <  1:290913/139‑1 (MQ=255)                                tttCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCgg                                                                                                <  1:658325/139‑1 (MQ=255)                                     aGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTAcc                                                                                           <  2:112915/139‑1 (MQ=255)                                       aaTGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:77418/139‑1 (MQ=255)                                       aaTGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  2:232968/139‑1 (MQ=255)                                        aTGACCCGCAGCGCGCATCTGAAGCAGGTAAAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCg                                                                                         <  1:743490/139‑1 (MQ=255)                                           aCCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggtgg                                                                                     >  1:81106/1‑139 (MQ=255)                                            cccGCAGCGCGCATCTGAAGCTGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCCGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCggtggt                                                                                    <  2:448834/139‑1 (MQ=255)                                                             aaGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   >  2:769127/1‑139 (MQ=255)                                                             aaGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   <  2:14960/139‑1 (MQ=255)                                                                  ggT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                                                   <  1:158947/71‑1 (MQ=255)                                                                  ggT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CAttt                                                                                                                                   >  2:158947/1‑71 (MQ=255)                                                                  ggT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              <  2:24959/139‑1 (MQ=255)                                                                  ggT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAg                                                              <  2:403784/139‑1 (MQ=255)                                                                    t‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCt                                                            >  2:629492/1‑139 (MQ=255)                                                                              tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   >  1:135848/1‑123 (MQ=255)                                                                              tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   <  2:135848/123‑1 (MQ=255)                                                                              tggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATg                                                   >  2:374048/1‑139 (MQ=255)                                                                               ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATa                                                                               <  1:299816/110‑1 (MQ=255)                                                                               ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATa                                                                               >  2:299816/1‑110 (MQ=255)                                                                               ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   >  2:630863/1‑122 (MQ=255)                                                                               ggtAAGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAAt                                                                   <  1:630863/122‑1 (MQ=255)                                                                                gtAAGGGCAGTCACGGCAAAAGCAACAACTAACCTGTATAATCAATAACGAAT‑CATTTTTG‑ATGTAGCTAGTCAAAAGGCCATCACCGCGGGTTAGCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATgcg                                                 <  2:309828/139‑1 (MQ=255)                                                                                  aaGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               <  1:708901/139‑1 (MQ=255)                                                                                  aaGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               <  1:769127/139‑1 (MQ=255)                                                                                  aaGAGCAGTCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGcgcg                                               <  2:601259/139‑1 (MQ=255)                                                                                          tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTg                                                                                  >  1:358800/1‑96 (MQ=255)                                                                                          tCACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTg                                                                                  <  2:358800/96‑1 (MQ=255)                                                                                           cACGGCAAAAGCGACAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATc                                      <  1:307104/139‑1 (MQ=255)                                                                                                        aCAACTAACCGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa                         <  2:598378/139‑1 (MQ=255)                                                                                                               accGGGCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCa                  <  1:63220/138‑1 (MQ=255)                                                                                                                   ggCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAatat              >  1:608747/1‑139 (MQ=255)                                                                                                                    gCTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGACGATTGCAatata             >  2:5701/1‑139 (MQ=255)                                                                                                                     cTAATCAATGACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAatatat            <  1:365504/139‑1 (MQ=255)                                                                                                                              gACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa                         >  2:637206/1‑117 (MQ=255)                                                                                                                              gACGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCagaa                         <  1:637206/117‑1 (MQ=255)                                                                                                                               aCGAAT‑CATTTTTG‑CTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCa  <  2:608747/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                       GTAAAAAAGGTGGACAGCACAGCGGGGGTAATTTCAAGAATGACCCGCAGCGCGCATCTGAAGCAGGT‑AAAAAAGGTGGTAAGAGCAGTCACGGCAAAAGCGACAACTAGCCGGGCTAATCAATGACGAATGCATTTTTGTCTGTAGCTCGTCAAAAAGCCATCACCGCCGGTTACCCGGTGGTTGATACTGATGACAAATGTAAGCTTGCCTGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCA  >  NC_000913/1068145‑1068410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑