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%	222.0 / NA	56	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 (21/35);  total (21/35)

ATATAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGACTCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACATCT  >  NZ_CP009273/59495‑59754                                                                                                                                     |                                                                                                                                atatAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCggg                                                                                                                            >  2:422627/1‑138 (MQ=255)    taAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                         <  1:610838/138‑1 (MQ=255)      agagACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                       <  1:422627/138‑1 (MQ=255)          aCGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTa                                                                                                                  >  1:661264/1‑139 (MQ=255)            ggTTAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACa                                                                                                                <  1:178161/139‑1 (MQ=255)            ggTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTAc                                                                                                                 >  1:676/1‑138 (MQ=255)                 aCGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAgg                                                                                                           <  2:284214/139‑1 (MQ=255)                 aCGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAgg                                                                                                           <  1:796136/139‑1 (MQ=255)                 aCGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAgg                                                                                                           <  1:451137/139‑1 (MQ=255)                      tGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGcc                                                                                                      <  2:7521/139‑1 (MQ=255)                        aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCa                                                                                                         >  2:675236/1‑134 (MQ=255)                        aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCa                                                                                                         <  1:675236/134‑1 (MQ=255)                        aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                    >  2:493222/1‑139 (MQ=255)                        aagaaAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCt                                                                                                    <  2:661264/139‑1 (MQ=255)                              aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                              <  2:38988/139‑1 (MQ=255)                              aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                              <  2:520297/139‑1 (MQ=255)                              aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                              <  1:294932/139‑1 (MQ=255)                              aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                              <  1:433093/139‑1 (MQ=255)                              aaGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGAt                                                                                              <  2:706885/139‑1 (MQ=255)                               aGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                       >  1:525676/1‑113 (MQ=255)                               aGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAttt                                                                                                                       <  2:525676/113‑1 (MQ=255)                                      aaaTTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGtat                                                                                      <  2:310179/139‑1 (MQ=255)                                             cTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTa                                                                               <  2:811900/139‑1 (MQ=255)                                                  gAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGa                                                                          <  2:710466/139‑1 (MQ=255)                                                   aGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                         >  2:841420/1‑91 (MQ=255)                                                   aGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGAt                                                                                                                         <  1:841420/91‑1 (MQ=255)                                                          aGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTa                                                                   >  2:711448/1‑138 (MQ=255)                                                          aGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTa                                                                   >  2:276963/1‑138 (MQ=255)                                                               aTTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATc                                                             >  2:145030/1‑139 (MQ=255)                                                                  aCCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACa                                                                                                                >  1:519029/1‑85 (MQ=255)                                                                  aCCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACa                                                                                                                <  2:519029/85‑1 (MQ=255)                                                                    cGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTg                                                        <  2:629439/139‑1 (MQ=255)                                                                      aaTGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGgc                                                      >  2:333554/1‑139 (MQ=255)                                                                      aaTGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGgc                                                      >  2:361975/1‑139 (MQ=255)                                                                             aGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTa                                                >  2:455780/1‑138 (MQ=255)                                                                             aGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTa                                                >  1:796774/1‑138 (MQ=255)                                                                              gCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTaaa                                              <  2:273853/139‑1 (MQ=255)                                                                                   gCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCa                                         <  1:333554/139‑1 (MQ=255)                                                                                   gCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGATATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCa                                         <  1:711448/139‑1 (MQ=255)                                                                                         cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATa                                       >  2:220402/1‑135 (MQ=255)                                                                                         cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATa                                       <  1:220402/135‑1 (MQ=255)                                                                                         cGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTAt                                   >  2:841619/1‑139 (MQ=255)                                                                                                acTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATa                            <  2:62170/139‑1 (MQ=255)                                                                                                    aaaGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGc                         <  2:694547/138‑1 (MQ=255)                                                                                                      aGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGcc                               >  2:233548/1‑130 (MQ=255)                                                                                                      aGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGcc                               <  1:233548/130‑1 (MQ=255)                                                                                                      aGCAGTTTGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCg                       >  2:12657/1‑138 (MQ=255)                                                                                                           tttGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATg                                                                                             <  2:447855/63‑1 (MQ=255)                                                                                                           tttGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATg                                                                                             >  1:447855/1‑63 (MQ=255)                                                                                                           tttGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATggg                 >  1:10974/1‑139 (MQ=255)                                                                                                           tttGGCAGAAACAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATggg                 <  1:252509/139‑1 (MQ=255)                                                                                                                     aCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCaa       <  2:844749/139‑1 (MQ=255)                                                                                                                     aCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCaa       <  1:276963/139‑1 (MQ=255)                                                                                                                     aCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCaa       <  1:530024/139‑1 (MQ=255)                                                                                                                     aCAAAAAATCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCaa       <  2:16961/139‑1 (MQ=255)                                                                                                                          aaaTCCCCGGAATCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACAtct  <  2:676/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                ATATAAGAGACGGTCAACGGGTGAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCAACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGACTCGGGGATTTATGTACAAGAGGCAGCCCTTAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCATACGCCGGATGGGTAATCGTCAACATCT  >  NZ_CP009273/59495‑59754

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑