Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	59,627	C→A	intergenic (‑153/+60)	BW25113_RS25400 ← / ← rluA	transposase/bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	59,627	0	C	A	100.0%	189.3 / NA	46	intergenic (‑153/+60)	BW25113_RS25400/rluA	transposase/bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (18/28);  total (18/28)

AATATAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGACTCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACATCTCTGCATG  >  NZ_CP009273/59494‑59761                                                                                                                                      |                                                                                                                                       aaTATAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCggg                                                                                                                                   <  2:459916/139‑1 (MQ=255)       agagACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                              <  2:33207/138‑1 (MQ=255)           aCGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                                >  2:269859/1‑132 (MQ=255)           aCGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                                <  1:269859/132‑1 (MQ=255)            cGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTa                                                                                                                         >  2:372278/1‑138 (MQ=255)             ggTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTAc                                                                                                                        >  2:452486/1‑138 (MQ=255)             ggTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTAc                                                                                                                        >  2:270769/1‑138 (MQ=255)                  aCGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAgg                                                                                                                  <  1:457102/139‑1 (MQ=255)                   cGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGc                                                                                                                 <  1:423292/139‑1 (MQ=255)                    gggTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCa                                                                                                                <  1:607594/139‑1 (MQ=255)                     ggTGAAGAAAAGGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAg                                                                                                               <  2:116864/139‑1 (MQ=255)                     ggTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAg                                                                                                               <  2:357817/139‑1 (MQ=255)                       tGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGcc                                                                                                             >  1:67561/1‑139 (MQ=255)                       tGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGcc                                                                                                             <  2:15702/139‑1 (MQ=255)                        gaagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGccc                                                                                                            >  2:219688/1‑139 (MQ=255)                         aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                              >  1:459336/1‑120 (MQ=255)                         aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                              <  2:459336/120‑1 (MQ=255)                         aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                           >  1:346210/1‑139 (MQ=255)                         aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                           >  1:636358/1‑139 (MQ=255)                               aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTAGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                                     <  1:613131/139‑1 (MQ=255)                                aGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATg                                                                                                    <  1:513228/139‑1 (MQ=255)                                 gTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGa                                                                                                   <  2:67561/139‑1 (MQ=255)                                             gCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACg                                                                                        <  2:346210/138‑1 (MQ=255)                                              cTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTa                                                                                      <  2:151828/139‑1 (MQ=255)                                                   gAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGa                                                                                 <  1:219688/139‑1 (MQ=255)                                                   gAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGa                                                                                 <  1:452486/139‑1 (MQ=255)                                                           aGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                           <  2:590614/105‑1 (MQ=255)                                                           aGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                           >  1:590614/1‑105 (MQ=255)                                                                      gAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTgg                                                              <  2:406339/139‑1 (MQ=255)                                                                         tGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGgcgc                                                           >  1:63994/1‑139 (MQ=255)                                                                              aGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                                     <  1:136509/92‑1 (MQ=255)                                                                              aGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                                     >  2:136509/1‑92 (MQ=255)                                                                              aGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTa                                                       >  2:299133/1‑138 (MQ=255)                                                                                   aGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGt                                                  >  1:607708/1‑138 (MQ=255)                                                                                     ccACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCAt                                               <  1:215776/139‑1 (MQ=255)                                                                                         acGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTa                                           <  2:371620/139‑1 (MQ=255)                                                                                          cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                                <  1:494060/53‑1 (MQ=255)                                                                                          cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                                >  2:494060/1‑53 (MQ=255)                                                                                          cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTAt                                          <  2:607708/139‑1 (MQ=255)                                                                                                            tttGGCAGAAACAAAAAATCCCCGGAATCGGTGAttt                                                                                                                              <  2:164644/37‑1 (MQ=255)                                                                                                            tttGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                              >  1:164644/1‑37 (MQ=255)                                                                                                            tttGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATggg                        >  1:24102/1‑139 (MQ=255)                                                                                                                    aaaCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGt                 >  1:31416/1‑138 (MQ=255)                                                                                                                      aCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCaa              <  2:24102/139‑1 (MQ=255)                                                                                                                       cAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAAc             <  1:184695/139‑1 (MQ=255)                                                                                                                                  cGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACATCTCTGCATg  <  1:372278/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       AATATAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGACTCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACATCTCTGCATG  >  NZ_CP009273/59494‑59761

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑