Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,966,598	G→A	G61E (GGA→GAA)	rho →	transcription termination factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,966,598	0	G	A	93.8%	205.9 / 3.8	65	G61E (GGA→GAA)	rho	transcription termination factor
Reads supporting (aligned to +/- strand):  ref base G (2/2);  new base A (17/44);  total (19/46)
Fisher's exact test for biased strand distribution p-value = 5.74e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

CGTAAGCAGGACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGC  >  NC_000913/3966504‑3966692                                                                                               |                                                                                               cGTAAGCAGGACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTg                                                                                           >  2:2146321/1‑100 (MQ=255)     aGCAGGACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGttt                                                                                       <  2:633521/100‑1 (MQ=255)     aGCAGGACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGttt                                                                                       <  1:633521/100‑1 (MQ=255)         ggACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTtcctc                                                                                   <  2:755475/100‑1 (MQ=255)         ggACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTtcctc                                                                                   <  1:755475/100‑1 (MQ=255)           aCATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCg                                                                                 <  2:1132175/100‑1 (MQ=255)            cATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGt                                                                                >  2:2210232/1‑100 (MQ=255)            cATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGt                                                                                <  2:543450/100‑1 (MQ=255)            cATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGt                                                                                <  1:543450/100‑1 (MQ=255)              ttattTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTc                                                                              <  1:126516/100‑1 (MQ=255)              ttattTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTc                                                                              <  2:126516/100‑1 (MQ=255)                  ttttGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCa                                                                          <  2:2062607/100‑1 (MQ=255)                     tGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGAc                                                                       <  1:442209/100‑1 (MQ=255)                     tGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGAc                                                                       <  2:442209/100‑1 (MQ=255)                     tGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGAc                                                                       >  2:2136347/1‑100 (MQ=255)                       ccATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAg                                                                     <  2:1060092/100‑1 (MQ=255)                           ccTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTcc                                                                 <  1:18332/100‑1 (MQ=255)                           ccTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTcc                                                                 <  2:1791195/100‑1 (MQ=255)                           ccTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTcc                                                                 <  2:18332/100‑1 (MQ=255)                              gAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTAc                                                              <  2:2289369/100‑1 (MQ=255)                               aaGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTAcc                                                             <  2:534880/100‑1 (MQ=255)                               aaGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTAcc                                                             <  1:534880/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        <  1:489483/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        <  2:489483/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        <  2:477019/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        >  2:1049253/1‑100 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        <  1:477019/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGcc                                                        <  2:1207836/100‑1 (MQ=255)                                    gcaCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAACTCCTACCTCGcc                                                        <  2:1515851/100‑1 (MQ=255)                                      aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCgg                                                      <  2:1552280/100‑1 (MQ=255)                                      aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCgg                                                      <  2:731450/100‑1 (MQ=255)                                      aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCgg                                                      <  1:731450/100‑1 (MQ=255)                                      aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCgg                                                      >  2:565870/1‑100 (MQ=255)                                      aCGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCgg                                                      >  1:565870/1‑100 (MQ=255)                                       cGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGt                                                     >  2:1719944/1‑100 (MQ=255)                                         cAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTcc                                                   <  2:12300/100‑1 (MQ=255)                                         cAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTcc                                                   <  1:12300/100‑1 (MQ=255)                                              agTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatg                                              <  2:58477/100‑1 (MQ=255)                                              agTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatg                                              <  1:58477/100‑1 (MQ=255)                                              agTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatg                                              <  1:11138/100‑1 (MQ=255)                                              agTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatg                                              <  2:11138/100‑1 (MQ=255)                                               gTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatga                                             <  2:762018/100‑1 (MQ=255)                                               gTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCtgatga                                             <  1:762018/100‑1 (MQ=255)                                                       gATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACg                                     >  2:962137/1‑100 (MQ=255)                                                       gATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACg                                     <  2:722965/100‑1 (MQ=255)                                                       gATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACg                                     <  1:722965/100‑1 (MQ=255)                                                             tttGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTccc                               <  2:411434/100‑1 (MQ=255)                                                             tttGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTccc                               <  1:411434/100‑1 (MQ=255)                                                               tGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCt                             <  2:2054224/100‑1 (MQ=255)                                                               tGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCt                             >  2:834810/1‑100 (MQ=255)                                                               tGGTGATGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCt                             >  1:834810/1‑100 (MQ=255)                                                                    aTGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCa                        <  2:781003/100‑1 (MQ=255)                                                                    aTGGCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCa                        <  1:781003/100‑1 (MQ=255)                                                                      ggCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCaaa                      >  2:606966/1‑100 (MQ=255)                                                                      ggCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCaaa                      >  1:502979/1‑100 (MQ=255)                                                                      ggCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCaaa                      >  1:606966/1‑100 (MQ=255)                                                                      ggCGTACTGGAGATATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCaaa                      >  2:502979/1‑100 (MQ=255)                                                                            cTGGAGATATTGCAGCATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATccgcc                <  2:2527662/100‑1 (MQ=255)                                                                                agaTATTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGttt            >  2:1251680/1‑100 (MQ=255)                                                                                    atTGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAAc        >  2:1267478/1‑100 (MQ=255)                                                                                     ttGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAAcc       <  2:2214390/100‑1 (MQ=255)                                                                                      tGCAGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCt      >  2:1398524/1‑100 (MQ=255)                                                                                       gCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTc     >  1:404100/1‑100 (MQ=255)                                                                                       gCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTc     >  2:404100/1‑100 (MQ=255)                                                                                         aGGATGAATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCg   <  2:2241147/100‑1 (MQ=255)                                                                                          ggatgaatTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGc  >  1:789651/1‑100 (MQ=255)                                                                                          ggatgaatTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGc  >  2:789651/1‑100 (MQ=255)                                                                                               |                                                                                               CGTAAGCAGGACATTATTTTTGCCATCCTGAAGCAGCACGCAAAGAGTGGCGAAGATATCTTTGGTGATGGCGTACTGGAGATATTGCAGGATGGATTTGGTTTCCTCCGTTCCGCAGACAGCTCCTACCTCGCCGGTCCTGATGACATCTACGTTTCCCCTAGCCAAATCCGCCGTTTCAACCTCCGC  >  NC_000913/3966504‑3966692

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑