Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,380,730	T→A	15.8%	intergenic (‑112/+23)	PP_t67 ← / ← PP_t66	tRNA‑Met/tRNA‑Met

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,380,730	0	T	A	15.8%	129.8 / 14.9	51	intergenic (‑112/+23)	PP_t67/PP_t66	tRNA‑Met/tRNA‑Met
Reads supporting (aligned to +/- strand):  ref base T (22/20);  new base A (4/4);  total (26/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

AGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCAAGCGCTAGGC  >  NC_002947/1380601‑1380878                                                                                                                                  |                                                                                                                                                       aGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGaa                                                                                                                                  >  2:948669/1‑150 (MQ=255)  ggCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGCAt                                                                                                                                 <  1:948669/150‑1 (MQ=255)  ggCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAAt                                                                                                                                 >  1:168518/1‑150 (MQ=255)     tgctCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTg                                                                                                                              <  2:606079/150‑1 (MQ=255)        tCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGT‑TAACACAGTGGCC‑tttttcttt                                                                                                                                   <  1:610056/142‑6 (MQ=21)        tCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGT‑TAACACAGTGGCC‑tttttcttt                                                                                                                                   >  2:610056/1‑137 (MQ=21)            tCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTGTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCgg                                                                                                                       <  1:1121573/150‑1 (MQ=255)            tCCCGCGTCAGTGGGGCGGATTCTAAAGTGGGCGGTTTGTGTGTCAAGGGCTAGGCTTGGATATTTCGACGTGTTTTCGCGAATGCTAATCAACAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑ATATCTTGAATCTGGTTGCgg                                                                                                                       >  2:361526/1‑150 (MQ=18)               cgcgTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTgg                                                                                                                                               <  2:351508/124‑1 (MQ=255)               cgcgTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTgg                                                                                                                                               >  1:351508/1‑124 (MQ=255)                     aGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGAt                                                                                                              <  1:315829/150‑1 (MQ=255)                      gTGGGGAGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGAtt                                                                                                             >  2:547697/1‑150 (MQ=255)                          ggCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGaa                                                                                                         >  2:612968/1‑150 (MQ=255)                           gCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTTAAC‑ACAGTGGCC‑tttttcttt                                                                                                                                   >  1:985036/1‑118 (MQ=25)                           gCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGT‑TAACACAGTGGCC‑tttttcttt                                                                                                                                   >  1:984976/1‑118 (MQ=25)                           gCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGT‑TAACACAGTGGCC‑tttttcttt                                                                                                                                   <  2:984976/123‑6 (MQ=25)                           gCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGT‑TAACACAGTGGCC‑tttttcttt                                                                                                                                   <  2:985036/123‑6 (MQ=25)                           gCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGAAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCT‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAAc                                                                                                        >  1:775895/1‑150 (MQ=255)                                     cAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAAcc                                                                                                       >  1:530792/1‑141 (MQ=255)                                     cAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAAcc                                                                                                       <  2:530792/141‑1 (MQ=255)                                        tgtgtgGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGc                                                                                                                                              <  1:1142515/100‑1 (MQ=255)                                        tgtgtgGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGc                                                                                                                                              >  2:1142515/1‑100 (MQ=255)                                        tgtgtgGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTATTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCgg                                                                                           <  2:1053653/150‑1 (MQ=255)                                             ggTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTAt                                                                                      <  1:860219/150‑1 (MQ=255)                                             gctttGTATGTCAAGCGCTAGTTTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTTGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTAt                                                                                      <  1:495307/148‑1 (MQ=255)                                                   tATGTCAAGCGCTAGGCTTTGATTTTTTTATTTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGccc                                                                                >  2:477265/1‑150 (MQ=255)                                                             gcTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTAc                                                                      <  1:547697/150‑1 (MQ=255)                                                              cTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑AAAGTGGCC‑TTTTCTTGAATGTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACAAGCTaac                                                                     >  2:305667/1‑148 (MQ=255)                                                                 ggCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCAGGAGCCTGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAgg                                                                  <  2:168518/150‑1 (MQ=255)                                                                    tttGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCtt                                                                                                                                     >  1:4061/1‑80 (MQ=255)                                                                    tttGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCtt                                                                                                                                     <  2:4061/80‑1 (MQ=255)                                                                       gATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTc                                                            >  1:1029901/1‑150 (MQ=255)                                                                                     ttttCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTa                                                                       <  2:57381/125‑1 (MQ=255)                                                                                     ttttCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTa                                                                       >  1:57381/1‑125 (MQ=255)                                                                                       ttCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTgg                                            <  2:1029901/150‑1 (MQ=255)                                                                                         cgcgAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTGCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTgggg                                          <  1:361526/150‑1 (MQ=255)                                                                                                gCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTc                                   >  2:354770/1‑150 (MQ=255)                                                                                                      cagcagGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTa                                 <  1:1191397/146‑1 (MQ=255)                                                                                                      cagcagGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTa                                 >  2:1191397/1‑146 (MQ=255)                                                                                                       agcagGCAAAGAAAAACGCCACTGAGCTA‑ACAGTGGCC‑TTTTCTTGCATCGGTTTGCGGGATCCGGATTTGAACCGACGACCTTCGCGTTATGATCCCCACGAGCTACCTGACTTCCCCCCCCCACGGCAGTGGGGCGGATTCTACAggg                            >  2:169982/1‑148 (MQ=14)                                                                                                            gCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAg                       <  1:477265/150‑1 (MQ=255)                                                                                                            gCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAg                       <  1:354770/150‑1 (MQ=255)                                                                                                              aaaGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGGCAGGGGGGCGGATTCTACAGCGTGTCGtt                     >  1:233593/1‑150 (MQ=255)                                                                                                               aaGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAg                                                                          <  2:197952/96‑1 (MQ=39)                                                                                                               aaGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAg                                                                          >  1:197952/1‑96 (MQ=39)                                                                                                                 gAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTtat                  >  2:1092840/1‑150 (MQ=255)                                                                                                                   aacatgCCACTGCGTGA‑ACATTTTCC‑TTTTCGTGAATCTGGTTTCGGGAGCCGGATTTGAACCGACGTCCTTCGGGTTATGAGCCCGACGGGCGACCTGTTTGCTACATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTatat                <  2:233593/145‑1 (MQ=14)                                                                                                                     aaGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGt              >  1:178827/1‑150 (MQ=255)                                                                                                                     aaGGCCACTGT‑TAACACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTatat                <  1:191438/148‑1 (MQ=255)                                                                                                                       ggCCACTGTTAAC‑ACAGTGGCCTTTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGGAGTTTATATGTc             >  1:1151557/1‑150 (MQ=17)                                                                                                                       ggCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCa            >  1:1075665/1‑150 (MQ=255)                                                                                                                                 ttA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGc                             <  2:1100341/123‑1 (MQ=255)                                                                                                                                 ttA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGc                             >  1:1100341/1‑123 (MQ=255)                                                                                                                                 ttA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCAAGCGCTAg    <  2:1153928/148‑1 (MQ=255)                                                                                                                                 ttA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCAAGCGCTAGGc  >  2:1009857/1‑150 (MQ=255)                                                                                                                                 ttA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCACGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCAAGCGCTAg    >  1:1153928/1‑148 (MQ=255)                                                                                                                                  |                                                                                                                                                       AGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGTGTGTGGTTTGTATGTCAAGCGCTAGGCTTTGATTTTTCGACGTTTTTTCGCGAATGCTTATCAGCAGGCAAAGAAAAAGGCCACTGTGTTA‑ACAGTGGCC‑TTTTCTTGAATCTGGTTGCGGGAGCCGGATTTGAACCGACGACCTTCGGGTTATGAGCCCGACGAGCTACCAGGCTGCTCCATCCCGCGTCAGTGGGGCGGATTCTACAGCGTGTAGTTTATATGTCAAGCGCTAGGC  >  NC_002947/1380601‑1380878

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑