Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,583,454	G→A	intergenic (+36/‑29)	yrhA → / → insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,583,454	0	G	A	100.0%	115.8 / NA	37	intergenic (+36/‑29)	yrhA/insA	pseudogene, interrupted by IS1E/IS1 repressor TnpA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/15);  total (22/15)

TATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCG  >  NC_000913/3583335‑3583558                                                                                                                        |                                                                                                         tataGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGa                                                                                       >  2:1840462/1‑139 (MQ=255)                 atTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                       >  1:990431/1‑139 (MQ=255)                 atTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                       <  1:1840462/139‑1 (MQ=255)                             cTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCa                                                           <  2:990431/139‑1 (MQ=255)                              tGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAg                                                          >  1:324758/1‑139 (MQ=255)                               gATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGc                                                         >  1:1755013/1‑139 (MQ=255)                                  cTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGt                                                      <  1:1481601/139‑1 (MQ=255)                                     cAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTccc                                                   >  1:1795122/1‑139 (MQ=255)                                      aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                     <  1:47591/104‑1 (MQ=255)                                      aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                     >  2:47591/1‑104 (MQ=255)                                      aaGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcct                                                  >  1:1525843/1‑139 (MQ=255)                                          aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                              >  1:1022101/1‑139 (MQ=255)                                          aCGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTg                                              >  2:438282/1‑139 (MQ=255)                                             gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                <  2:462976/134‑1 (MQ=255)                                             gTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                >  1:462976/1‑134 (MQ=255)                                                    aTCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                     >  1:1805102/1‑90 (MQ=255)                                                    aTCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAgg                                                                                     <  2:1805102/90‑1 (MQ=255)                                                            ttATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                <  1:1841194/135‑1 (MQ=255)                                                            ttATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACg                                >  2:1841194/1‑135 (MQ=255)                                                             tataGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGggtg                           >  2:1983228/1‑139 (MQ=255)                                                                aGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGgtggtg                        >  1:1838403/1‑139 (MQ=255)                                                                   aTTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                             >  1:1193048/1‑131 (MQ=255)                                                                   aTTTCAATAGTTACTTATGACATTAAAGGTGATGCTGCCATCTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCGCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACgggg                             <  2:1193048/131‑1 (MQ=255)                                                                     ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                     >  1:437223/1‑89 (MQ=255)                                                                     ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCt                                                                     <  2:437223/89‑1 (MQ=255)                                                                     ttCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTaa                   >  1:377090/1‑139 (MQ=255)                                                                         atatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                >  1:1003558/1‑106 (MQ=255)                                                                         atatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCcctcc                                                <  2:1003558/106‑1 (MQ=255)                                                                          tatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAg                                                                                      <  2:636528/67‑1 (MQ=255)                                                                          tatTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAg                                                                                      >  1:636528/1‑67 (MQ=255)                                                                                      aCATTAATGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                       <  2:1224392/70‑1 (MQ=11)                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCAccgccg  <  2:1755013/139‑1 (MQ=25)                                                                                      aCATTAAAGGTGATGCTGCCAACTTACTGATTGAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCtt                                                                       >  1:1224392/1‑70 (MQ=255)                                                                                        aTTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                                    >  2:17724/1‑71 (MQ=255)                                                                                        aTTAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTg                                                                    <  1:17724/71‑1 (MQ=255)                                                                                          tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGt                                                                   >  1:356888/1‑70 (MQ=25)                                                                                          tAAAGGTGATGCTGCCAACTTACTGATTTAATGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGt                                                                   <  2:356888/70‑1 (MQ=255)                                                                                                                        |                                                                                                         TATAGAAATAATGATGATTTCATAAACCCTGATCTACAAGAACGGTTAGTGATCGGGGATTATAGCATTTCAATATTTACTTATGACATTAAAGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTTGAGGTGCTCCAGTGGCTTCTGTTTCTATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACCGCCG  >  NC_000913/3583335‑3583558

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑