Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,950,420	G→A	*33* (TAG→TAA)	ilvL →	ilvG operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,950,420	0	G	A	100.0%	217.4 / NA	66	*33* (TAG→TAA)	ilvL	ilvG operon leader peptide
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/32);  total (34/32)

GGCATTCCTTCGAACAAGATGCAAGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAA  >  NC_000913/3950287‑3950553                                                                                                                                      |                                                                                                                                       ggCATTCCTTCGAACAAGATGCAAGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATc                                                                                                                                   >  1:1157450/1‑139 (MQ=255)          tCGAACAAGATGCAAGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTaa                                                                                                                          <  1:593411/139‑1 (MQ=255)                  gATGCAAGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTaa                                                                                                                  >  2:632859/1‑139 (MQ=255)                       aaGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑ccc                                                                                                            <  1:879923/139‑1 (MQ=255)                        aGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑cccc                                                                                                           >  1:120235/1‑139 (MQ=255)                                 aaaaTGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  <  2:1157450/139‑1 (MQ=255)                                 aaaaTGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  <  1:632859/139‑1 (MQ=255)                                    aTGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAg                                                                                                                 <  1:1014319/122‑1 (MQ=255)                                    aTGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAg                                                                                                                 >  2:1014319/1‑122 (MQ=255)                                                cTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGtttt                                                                                   >  1:750733/1‑139 (MQ=255)                                                      gTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGa                                                                             >  1:18042/1‑139 (MQ=255)                                                       tGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGAc                                                                            <  2:18042/139‑1 (MQ=255)                                                        gATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAAc                                                                                                                         <  1:962452/94‑1 (MQ=255)                                                        gATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAAc                                                                                                                         >  2:962452/1‑94 (MQ=255)                                                         aTTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGAt                                                                                                                                    <  2:361685/82‑1 (MQ=255)                                                         aTTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGAt                                                                                                                                    >  1:361685/1‑82 (MQ=255)                                                                  gTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGACCCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACa                                                                  >  1:524785/1‑139 (MQ=255)                                                                   tCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATa                                                                >  1:473675/1‑139 (MQ=255)                                                                       gATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGACCCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAAcc                                                             <  2:524785/139‑1 (MQ=255)                                                                       gATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCg                                                            >  1:182539/1‑139 (MQ=255)                                                                            gCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACa                                                                  >  1:1395858/1‑128 (MQ=255)                                                                            gCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACa                                                                  <  2:1395858/128‑1 (MQ=255)                                                                            gCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCgaggag                                                       <  2:37854/139‑1 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCtt                                                                         <  2:1059466/120‑1 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCtt                                                                         >  1:1059466/1‑120 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAAcc                                                             <  1:1074628/132‑1 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAAcc                                                             >  2:1074628/1‑132 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGc                                                      >  1:767103/1‑139 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGc                                                      >  2:1113451/1‑139 (MQ=255)                                                                             cGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGc                                                      <  2:473675/139‑1 (MQ=255)                                                                               tggtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  >  1:242063/1‑93 (MQ=255)                                                                               tggtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  <  2:242063/93‑1 (MQ=255)                                                                               tggtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGG‑TTTTTTTGACCTTAAAAACATAACCGAGGAGCAGa                                                   <  2:120235/139‑1 (MQ=255)                                                                                 gtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                              <  1:762238/111‑1 (MQ=255)                                                                                 gtggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                              >  2:762238/1‑111 (MQ=255)                                                                                  tggtgATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑ccc                                                                                                            <  2:1004538/80‑1 (MQ=255)                                                                                  tggtgATTATTATCCCACCCTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑ccc                                                                                                            >  1:1004538/1‑80 (MQ=255)                                                                                       attattATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCga                                                           >  2:965951/1‑124 (MQ=255)                                                                                       attattATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCga                                                           <  1:965951/124‑1 (MQ=255)                                                                                              tCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATaa                                         <  2:653813/135‑1 (MQ=255)                                                                                              tCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATaa                                         >  1:653813/1‑135 (MQ=255)                                                                                               cccACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑ccccc                                                                                                          >  1:435410/1‑69 (MQ=255)                                                                                               cccACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑ccccc                                                                                                          <  2:435410/69‑1 (MQ=255)                                                                                                   ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  >  1:919752/1‑73 (MQ=255)                                                                                                   ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  <  2:919752/73‑1 (MQ=255)                                                                                                   ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  >  1:499700/1‑73 (MQ=255)                                                                                                   ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGaa                                                                                                  <  2:499700/73‑1 (MQ=255)                                                                                                   ccGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACaaa                                >  2:586733/1‑139 (MQ=255)                                                                                                    cGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACaaaa                               <  1:586733/139‑1 (MQ=255)                                                                                                     gTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGa                                                                                                                       >  2:168284/1‑51 (MQ=255)                                                                                                     gTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGa                                                                                                                       <  1:168284/51‑1 (MQ=255)                                                                                                      tGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAAtt                             >  2:817906/1‑139 (MQ=255)                                                                                                      tGCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAAGAGCAGACAATGAATAACAGCACAAAAtt                             >  1:404011/1‑139 (MQ=255)                                                                                                       gCGGGGCTGCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAAGAGCAGACAATGAATAACAGCACAAAATTc                            <  2:404011/139‑1 (MQ=255)                                                                                                               gCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                              >  1:1236756/1‑81 (MQ=255)                                                                                                               gCACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTg                                                                              <  2:1236756/81‑1 (MQ=255)                                                                                                                cACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTaaa                                                                      <  1:1206774/88‑1 (MQ=255)                                                                                                                cACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTaaa                                                                      >  2:1206774/1‑88 (MQ=255)                                                                                                                cACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGc                                                      >  2:82984/1‑104 (MQ=255)                                                                                                                cACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGc                                                      <  1:82984/104‑1 (MQ=255)                                                                                                                cACTTGGACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCa                   >  2:103035/1‑139 (MQ=255)                                                                                                                     ggACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCa                   <  1:621276/134‑1 (MQ=255)                                                                                                                     ggACGAGGAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCa                   >  2:621276/1‑134 (MQ=255)                                                                                                                           ggAAAGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGAc        >  1:1096957/1‑139 (MQ=255)                                                                                                                             aaaGGCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACgg      <  1:103035/139‑1 (MQ=255)                                                                                                                                 gCTTAAAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGaa  <  2:767103/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       GGCATTCCTTCGAACAAGATGCAAGAAAAGACAAAATGACAGCCCTTCTACGAGTGATTAGCCTGGTCGTGATTAGCGTGGTGGTGATTATTATCCCACCGTGCGGGGCTGCACTTGGACGAGGAAAGGCTTAGAGATCAAGCCTTAACGAACTAAGA‑CCCCCGCACCGAAAGGTCCGGGGGTTTTTTTTGACCTTAAAAACATAACCGAGGAGCAGACAATGAATAACAGCACAAAATTCTGTTTCTCAAGATTCAGGACGGGGAA  >  NC_000913/3950287‑3950553

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑