Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,474,138	(A)6→7	coding (15/594 nt)	bdcR →	transcriptional repressor for divergent bdcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,474,132	1	.	A	96.7%	192.3 / ‑0.9	61	coding (9/594 nt)	bdcR	transcriptional repressor for divergent bdcA
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base A (31/28);  total (32/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.18e-01

CCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473998‑4474261                                                                                                                                        |                                                                                                                                  ccGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaa                                                                                                                               >  2:1186229/1‑139 (MQ=255)    aTACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaaaaa                                                                                                                            >  2:55248/1‑138 (MQ=255)            aCTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     <  1:1186229/139‑1 (MQ=255)                                  gTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaaaaaca                                                                                                                          >  2:796463/1‑108 (MQ=255)                                  gTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑aaaaaaaca                                                                                                                          <  1:796463/111‑4 (MQ=255)                                           gTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  2:128318/1‑107 (MQ=255)                                           gTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  1:128318/107‑1 (MQ=255)                                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             >  1:436803/1‑130 (MQ=255)                                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             <  2:436803/130‑1 (MQ=255)                                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGa                                                                                    >  1:1356846/1‑139 (MQ=255)                                             aaaaGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGa                                                                                    >  2:473514/1‑139 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAgg                                                                                                            >  2:109056/1‑95 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAgg                                                                                                            <  1:109056/95‑1 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             >  2:560210/1‑110 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGttt                                                                                             <  1:560210/110‑1 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                >  2:1030335/1‑139 (MQ=255)                                                                 cTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                >  2:1417677/1‑139 (MQ=255)                                                                           tatGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCtttt                                                      >  2:1427896/1‑139 (MQ=255)                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAAtctc                                                                        <  1:762270/112‑1 (MQ=255)                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAAtctc                                                                        >  2:762270/1‑112 (MQ=255)                                                                                    tGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                             >  1:1045631/1‑139 (MQ=255)                                                                                     gCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  1:664237/1‑65 (MQ=255)                                                                                     gCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  2:664237/65‑1 (MQ=255)                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCa                                                   >  2:91777/1‑130 (MQ=255)                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCa                                                   <  1:91777/130‑1 (MQ=255)                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                             <  2:1028063/136‑1 (MQ=255)                                                                                       aTTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCaaaa                                             >  1:1028063/1‑136 (MQ=255)                                                                                         tACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGtt                                        >  1:323552/1‑139 (MQ=255)                                                                                         tACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGtt                                        >  2:595036/1‑139 (MQ=255)                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     <  1:342579/57‑1 (MQ=255)                                                                                              aaCTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTcg                                                                                                                     >  2:342579/1‑57 (MQ=255)                                                                                                cTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGc                                 >  2:931274/1‑139 (MQ=255)                                                                                                   ttttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGt                              <  1:473514/139‑1 (MQ=255)                                                                                                     ttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      <  2:1029038/49‑1 (MQ=255)                                                                                                     ttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAAtctc                                                                                                                      >  1:1029038/1‑49 (MQ=255)                                                                                                     ttAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCa                            >  1:312512/1‑139 (MQ=255)                                                                                                      tAACTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAg                           <  2:1045631/139‑1 (MQ=255)                                                                                                        aCTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                <  2:1191590/100‑1 (MQ=255)                                                                                                        aCTTTCTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaa                                                                >  1:1191590/1‑100 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           >  2:63392/1‑52 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           <  1:63392/52‑1 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                   <  2:291500/76‑1 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAg                                                                                   >  1:291500/1‑76 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                  <  1:1348810/60‑1 (MQ=255)                                                                                                             cTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGa                                                                                                  >  2:1348810/1‑60 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           >  2:1257145/1‑42 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGgt                                                                                                           <  1:1257145/42‑1 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTcc                                                                                       <  2:116587/62‑1 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTcc                                                                                       >  1:116587/1‑62 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGtt              <  1:658024/135‑1 (MQ=255)                                                                                                                       gTTTTGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGtt              >  2:658024/1‑135 (MQ=255)                                                                                                                        ttttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGa         <  1:1417677/139‑1 (MQ=255)                                                                                                                         tttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAt        <  2:323552/139‑1 (MQ=255)                                                                                                                          ttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaa                                                               <  2:134568/83‑1 (MQ=255)                                                                                                                          ttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCaaa                                                               >  1:134568/1‑83 (MQ=255)                                                                                                                          ttGTAATGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGAtt       >  2:655192/1‑139 (MQ=255)                                                                                                                              aaTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCt   <  1:1427896/139‑1 (MQ=255)                                                                                                                               aTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCtt  <  1:595036/139‑1 (MQ=255)                                                                                                                               aTGGTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCtt  <  1:1030335/139‑1 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTc                                                                                        >  2:761925/1‑50 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTc                                                                                        <  1:761925/50‑1 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCTGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTCCTGATTATCt   <  2:556067/135‑1 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                     >  1:6767/1‑85 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCttttt                                                     <  2:6767/85‑1 (MQ=255)                                                                                                                                  gTCACTAAAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCt   >  1:556067/1‑135 (MQ=255)                                                                                                                                        |                                                                                                                                  CCGATACCACGACTGCCACCGAGGATGAGAACTGTCTTACCTGTAAAAGCGCCCATAAGGACTCCTTGATTTATTATGTAACATGCATTACAAAACTGTTTTAACTTTCTGTCAACAGGTTTTGTAATGGTCACT‑AAAAAACAATCTCGCGTTCCAGGTCGTCCCAGACGTTTCGCTCCTGAGCAGGCAATCTCTGCGGCAAAAGTGCTTTTTCACCAAAAAGGTTTCGATGCTGTCAGTGTTGCTGAAGTTACTGATTATCTT  >  NC_000913/4473998‑4474261

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: ‑