Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	BS168_reference_genome	4,140,276	C→A	10.5%	P6H (CCC→CAC)	rapG →	response regulator aspartate phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	4,140,276	0	C	A	10.5%	126.2 / 2.3	45	P6H (CCC→CAC)	rapG	response regulator aspartate phosphatase
Reads supporting (aligned to +/- strand):  ref base C (20/20);  new base A (3/2);  total (23/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGTCATATCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGCTTGCCTACTT  >  BS168_reference_genome/4140143‑4140414                                                                                                                                      |                                                                                                                                           ttGTCATATCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTAACATGAATAAGATCGAACCCg                                                                                                                                          >  7:215137/1‑136 (MQ=255)   gTCATATCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGa                                                                                                                                      <  2:22179/138‑1 (MQ=255)      atatCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATc                                                                                                                                  >  1:149335/1‑139 (MQ=255)      atatCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATc                                                                                                                                  >  7:154829/1‑139 (MQ=255)      atatCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATc                                                                                                                                  >  5:60568/1‑139 (MQ=255)             ctctcCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCa                                                                                                                           <  7:77355/139‑1 (MQ=255)             ctctcCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCa                                                                                                                           >  8:100493/1‑139 (MQ=255)                tcCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCa                                                                                                                           <  8:145074/136‑1 (MQ=255)                  cTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATg                                                                                                                         <  7:100493/136‑1 (MQ=255)                   ttCATATATTGACTAGAGGATTTTACATAAAATAGAAAGACGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGACACTAGATAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATtctc                                                                                                                      >  1:24112/1‑138 (MQ=255)                     cATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCa                                                                                                                     <  1:99766/137‑1 (MQ=255)                     cATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCa                                                                                                                     <  3:34584/137‑1 (MQ=255)                     cATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGAATCATAAGTCACTAGAGTAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTACCATGCTCaa                                                                                                                    <  4:91037/138‑1 (MQ=255)                         tatTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGAt                                                                                                                <  4:163403/138‑1 (MQ=255)                          atTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGAtt                                                                                                               >  2:170787/1‑138 (MQ=255)                          atTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGAtt                                                                                                               <  1:58374/138‑1 (MQ=255)                          atTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGAtt                                                                                                               >  2:58374/1‑138 (MQ=255)                          atTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGAtt                                                                                                               <  1:170787/138‑1 (MQ=255)                          atTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTg                                                                                                              >  6:81151/1‑139 (MQ=255)                            tGACTAGAGGATGTTACATAAAATAGAAAGAGGTGTTACTATCGGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGCTTgg                                                                                                             >  4:98232/1‑138 (MQ=255)                             gACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTa                                                                                                           >  4:49002/1‑139 (MQ=255)                              aCTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACACGCAGAAATCGCTAGCATGCTCAACGATTGGTAc                                                                                                          >  6:194270/1‑139 (MQ=255)                              aCTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACACGCAGAAATCGCTAGCATGCTCAACGATTGGTAc                                                                                                          >  6:191096/1‑139 (MQ=255)                                 agagGATTTTACATAAAATAGTAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCa                                                                                                                     <  5:220084/125‑1 (MQ=255)                                 agagGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCa                                                                                                                     >  6:220084/1‑125 (MQ=255)                                       ttttACATAAAATAGAAAGAGGTGTTACAATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGATCAACTATTGGTACCTTGCCAt                                                                                                  >  1:113559/1‑138 (MQ=255)                                          tACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCaa                                                                                               <  2:34752/138‑1 (MQ=255)                                           aCATAAAATTGAAAGAGGTGTTACTATGAGAATAAGCATCTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAg                                                                                              <  2:24112/138‑1 (MQ=255)                                                      aaaGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCa                                                                                                                           <  4:221030/98‑1 (MQ=255)                                                      aaaGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCa                                                                                                                           >  3:221030/1‑98 (MQ=255)                                                               ttACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCAcc                                                                                                                                            <  7:56450/72‑1 (MQ=255)                                                               ttACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCAcc                                                                                                                                            >  8:56450/1‑72 (MQ=255)                                                                         aaTAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTg                                                                                                              <  8:107503/92‑1 (MQ=255)                                                                         aaTAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTg                                                                                                              >  7:107503/1‑92 (MQ=255)                                                                                   tGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAATCATGAAGTTGAAGCATCCTCCCGTTTATTTGAAGAAGt                                                     >  4:66273/1‑139 (MQ=255)                                                                                   tGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGt                                                     >  1:128727/1‑139 (MQ=255)                                                                                   tGAGAGTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGCAACATGAAGTTGAAGAATCCTCCCGTTTATTTGATGAAGt                                                     >  8:57407/1‑139 (MQ=255)                                                                                                  aCTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGa                                      <  6:60568/139‑1 (MQ=255)                                                                                                          aaGGAGTTTCACATGAATAAGATCGAACCCGCATAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATg                               >  6:68517/1‑138 (MQ=255)                                                                                                              aGTTTCACATGAATAAGCTCGCACCCGCAGAAATCGCGAGCATGCTCTACTATTGGTACCTTGACATCAAGAAAGATGAAGTTGAAGATTCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAaga                          <  3:98232/139‑1 (MQ=255)                                                                                                                tttCACATGAATAAGATCGCACACGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCATTTATTGGATGACATGGAagag                         >  1:22950/1‑138 (MQ=255)                                                                                                                             agctCGCACCCGCAGAACTCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAGACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGc            <  8:154829/135‑1 (MQ=255)                                                                                                                             aGATCGCACACGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGc            <  5:194270/138‑1 (MQ=255)                                                                                                                             aGATCGCACACGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGc            <  5:191096/138‑1 (MQ=255)                                                                                                                                  gCACCCGCAGAAATCGCTAGCATGCTCATCGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGACTTTATTGGATGACATGGAAGATGATCAGGAGGTGCTTGcc       <  7:61736/138‑1 (MQ=255)                                                                                                                                   cACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTAt                                                               <  4:125048/81‑1 (MQ=255)                                                                                                                                   cACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTAt                                                               >  3:125048/1‑81 (MQ=255)                                                                                                                                     cccGCAGAAATCGCTAGCATGCGCAACGATTGGTAGCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGCTTGCCTACt   <  1:43254/139‑1 (MQ=255)                                                                                                                                      ccGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTGTATTGGATGACATGGATGAGGATCAGGAGGTGCTTGCCTACtt  >  6:5312/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                           TTGTCATATCATCTCTCCTTCATATATTGACTAGAGGATTTTACATAAAATAGAAAGAGGTGTTACTATCAGAATAAGCAACTGAGATTGATAAGTCACTAGAGAAAGGAGTTTCACATGAATAAGATCGCACCCGCAGAAATCGCTAGCATGCTCAACGATTGGTACCTTGCCATCAAGAAACATGAAGTTGAAGAATCCTCCCGTTTATTTGAAGAAGTGAAGCCTTTATTGGATGACATGGAAGAGGATCAGGAGGTGCTTGCCTACTT  >  BS168_reference_genome/4140143‑4140414

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑