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%	137.9 / NA	43	A414T (GCC→ACC)	gspD	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/25);  total (18/25)

GCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457484‑3457751                                                                                                                                     |                                                                                                                                        gCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACa                                                                                                                                   <  2:655581/139‑1 (MQ=255)   gAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAat                                                                                                                                 >  1:1089378/1‑139 (MQ=255)             gTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  1:1303280/139‑1 (MQ=255)               tGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     <  1:333900/139‑1 (MQ=255)               tGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     <  2:558864/139‑1 (MQ=255)               tGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCa                                                                                                                     <  2:1316163/139‑1 (MQ=255)                  cgcACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  1:1060652/139‑1 (MQ=255)                            tttACCAATACCGGATTACTGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGcttct                                                                                                              >  1:1097604/1‑133 (MQ=255)                            tttACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGcttct                                                                                                              <  2:1097604/133‑1 (MQ=255)                              tACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGc                                                                                                      <  1:1078082/139‑1 (MQ=255)                                   aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  1:1296180/1‑122 (MQ=255)                                   aTACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  2:1296180/122‑1 (MQ=255)                                              ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                    >  1:88204/1‑125 (MQ=255)                                              ccGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGa                                                                                                    <  2:88204/125‑1 (MQ=255)                                                      tAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  2:688866/139‑1 (MQ=255)                                                       aaCGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCgcgc                                                                             <  1:833970/139‑1 (MQ=255)                                                              cgcCAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              <  2:888061/131‑1 (MQ=255)                                                              cgcAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCATCTTCAATGGCGACTGGGGAGTACTGCTTACcgcg                                                                              >  1:888061/1‑131 (MQ=255)                                                                        ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  2:960796/80‑1 (MQ=255)                                                                        ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  1:960796/1‑80 (MQ=255)                                                                        ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  1:1343251/85‑1 (MQ=255)                                                                        ggCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  2:1343251/1‑85 (MQ=255)                                                                          cTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaaaaa                                                          >  1:702579/1‑139 (MQ=255)                                                                                      aGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGc                                              <  2:1089378/139‑1 (MQ=255)                                                                                      aGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGc                                              <  2:702579/139‑1 (MQ=255)                                                                                        aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  >  1:848058/1‑69 (MQ=255)                                                                                        aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGc                                                                                                                  <  2:848058/69‑1 (MQ=255)                                                                                        aaTGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCa                                            >  1:557859/1‑139 (MQ=255)                                                                                          tggtggGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCAcc                                          <  1:607208/139‑1 (MQ=255)                                                                                                gATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       >  2:935834/1‑56 (MQ=255)                                                                                                gATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCg                                                                                                                       <  1:935834/56‑1 (MQ=255)                                                                                                  tCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCAt                                  >  2:1111034/1‑139 (MQ=255)                                                                                                    aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             >  2:828919/1‑78 (MQ=255)                                                                                                    aCCAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGa                                                                                             <  1:828919/78‑1 (MQ=255)                                                                                                      cAGCGCGAATCCTTCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGTCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaa                                                             <  1:261480/108‑1 (MQ=255)                                                                                                      cAGCGCGAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATaa                                                             >  2:261480/1‑108 (MQ=255)                                                                                                         cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTggg                                                                                               <  2:260516/71‑1 (MQ=255)                                                                                                         cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTggg                                                                                               >  1:260516/1‑71 (MQ=255)                                                                                                         cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                     >  2:473853/1‑129 (MQ=255)                                                                                                         cgcgAATCCTGCCTGGGATATGTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAg                                     <  1:473853/129‑1 (MQ=255)                                                                                                                              gTTTAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTcc      >  1:436437/1‑139 (MQ=255)                                                                                                                                ttAGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCtt    <  2:557859/139‑1 (MQ=255)                                                                                                                                  aGCACCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCa  >  2:681216/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                        GCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAATGGCATGGCCGCAGGCTTCTTCAATGGCGACTGGGGAGTACTGCTTACCGCGCTGGCCAGTAACAATAAAAATGACATCCTCGCCACCCCAAGCATCGTAACGCTGGATAATAAACTCGCGTCCTTCA  >  NC_000913/3457484‑3457751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑