Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,457,616	G→A	A414T (GCC→ACC)	gspD →	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,457,616	0	G	A	100.0%	122.6 / NA	39	A414T (GCC→ACC)	gspD	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/21);  total (18/21)

AAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCC  >  NC_000913/3457490‑3457747                                                                                                                               |                                                                                                                                    aaaaaCGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggca                                                                                                                         <  1:408007/139‑1 (MQ=255)       gTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                   <  1:729499/139‑1 (MQ=255)                        tACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGc                                                                                                  <  1:556284/139‑1 (MQ=255)                             aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTg                                                                                             >  2:356308/1‑139 (MQ=255)                                        ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGc                                                                                  >  1:1217599/1‑139 (MQ=255)                                                 aaCGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                         <  1:356308/139‑1 (MQ=255)                                                      tGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                         >  2:1150333/1‑118 (MQ=255)                                                      tGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                         <  1:1150333/118‑1 (MQ=255)                                                       gcgcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                         <  1:804420/133‑1 (MQ=255)                                                       gcgcAAGGTGTGGCTGATTATAAAAAGAATGGAGGGATCACCAGAGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                         >  2:804420/1‑133 (MQ=255)                                                                  ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGTCATGGCCGCAGGCTTCTTCAAt                                                                                                     >  2:1245172/1‑94 (MQ=255)                                                                  ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                     <  1:1245172/94‑1 (MQ=255)                                                                               aaGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCg                                           <  1:1124071/139‑1 (MQ=255)                                                                                  aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                <  2:709748/83‑1 (MQ=255)                                                                                  aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                >  1:709748/1‑83 (MQ=255)                                                                                     ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                     <  2:1319168/75‑1 (MQ=255)                                                                                     ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAAt                                                                                                     >  1:1319168/1‑75 (MQ=255)                                                                                     ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                >  1:717143/1‑80 (MQ=255)                                                                                     ggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                <  2:717143/80‑1 (MQ=255)                                                                                        gggATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCaa                                  <  1:320036/139‑1 (MQ=255)                                                                                         ggATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAatggca                                                                                                                         <  1:672665/51‑1 (MQ=255)                                                                                         ggATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                 <  2:1217599/139‑1 (MQ=255)                                                                                         ggATCACCAGCGCGAATCCTGCATGGGATATGTTTAGCACCTACAatggca                                                                                                                         >  2:672665/1‑51 (MQ=255)                                                                                              aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                 <  2:91468/134‑1 (MQ=255)                                                                                              aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                 >  1:91468/1‑134 (MQ=255)                                                                                               ccAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              <  2:35174/56‑1 (MQ=255)                                                                                               ccAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              >  1:35174/1‑56 (MQ=255)                                                                                                   cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              >  2:554987/1‑52 (MQ=255)                                                                                                   cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              <  1:554987/52‑1 (MQ=255)                                                                                                     cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              <  2:305744/50‑1 (MQ=255)                                                                                                     cgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                              >  1:305744/1‑50 (MQ=255)                                                                                                       aaTCCTGCCTGAGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTgg                   >  2:781510/1‑139 (MQ=255)                                                                                                                 gggATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                               <  1:731854/69‑1 (MQ=255)                                                                                                                 gggATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTa                                                                               >  2:731854/1‑69 (MQ=255)                                                                                                                       tGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                          <  1:697994/68‑1 (MQ=255)                                                                                                                       tGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                          >  2:697994/1‑68 (MQ=255)                                                                                                                       tGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTc   >  1:1087746/1‑139 (MQ=255)                                                                                                                        gTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTcc  >  1:919135/1‑139 (MQ=255)                                                                                                                            aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATg                                                                                                    <  1:1235889/37‑1 (MQ=255)                                                                                                                               |                                                                                                                                    AAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCC  >  NC_000913/3457490‑3457747

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: ‑