Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	BS168_reference_genome	1,317,152:1	+G	88.7%	intergenic (+23/+5)	phrA → / ← yjpA	secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	1,317,152	1	.	G	88.7%	130.4 / 3.2	45	intergenic (+23/+5)	phrA/yjpA	secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme
Reads supporting (aligned to +/- strand):  ref base . (1/1);  major base G (19/19);  minor base T (2/3);  total (22/23)
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

AGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑G‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTC  >  BS168_reference_genome/1317015‑1317275                                                                                                                                                |                                                                                                                              aGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑g‑g‑g                                                                                                                                <  2:238694/138‑1 (MQ=255)      tgttgCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGTAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑G‑‑G‑tcttt                                                                                                                       >  7:236743/1‑139 (MQ=255)                 gCGGTCGGGGTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATttcttc                                                                                                               <  1:290645/139‑1 (MQ=255)                       gggTTCAGCTTTACTCAGGTGATGGTTCATGCAGGGGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTc                                                                                                         <  2:239957/139‑1 (MQ=255)                         gTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCa                                                                                                       <  2:145645/139‑1 (MQ=255)                                  tACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACATAAGGGAAAACATTTCATATTGCGGAACGCAATCAAAAATGATGCATAAAAAAAGACACTG‑A‑‑G‑GTGT‑CTTTTTTATTTCTTAAGCTTCCAGTAGTTTAt                                                                                              >  3:183243/1‑139 (MQ=255)                                       aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATATAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGtac                                                                                         >  8:204411/1‑137 (MQ=255)                                       aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑AGGG‑G‑G‑‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           <  7:61134/137‑1 (MQ=255)                                       aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           <  1:269540/137‑1 (MQ=255)                                         gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc                                                                                       >  4:4547/1‑139 (MQ=255)                                         gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc                                                                                       >  8:89070/1‑139 (MQ=255)                                         gTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc                                                                                       >  4:125658/1‑139 (MQ=255)                                               gTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCaga                                                                                  <  6:84541/138‑1 (MQ=255)                                                 tCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCag                                                                                   >  8:238086/1‑135 (MQ=255)                                                   aTGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATc                                                                             >  5:97879/1‑139 (MQ=255)                                                    tGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCGTTTATCGTCAGCTCAGAAGATcc                                                                            >  1:145519/1‑139 (MQ=255)                                                         gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAA‑‑G‑G‑GT‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTg                                                                       >  4:201502/1‑139 (MQ=255)                                                         gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           >  1:222139/1‑119 (MQ=255)                                                         gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGt                                                                                           <  2:222139/119‑1 (MQ=255)                                                         gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAATCTACACTTg                                                                       >  2:273496/1‑139 (MQ=255)                                                         gTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTg                                                                       >  8:186281/1‑139 (MQ=255)                                                          tGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCa                                                                                                       <  3:255140/106‑1 (MQ=255)                                                          tGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCa                                                                                                       >  4:255140/1‑106 (MQ=255)                                                             aaCAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGccac                                                                   <  7:21814/139‑1 (MQ=255)                                                                         aGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGc                                                       >  4:223517/1‑139 (MQ=255)                                                                          gAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCa                                                      <  7:89070/139‑1 (MQ=255)                                                                           aaGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCAACTTGCCACCAGCGGATCAGCAt                                                     >  5:70938/1‑139 (MQ=255)                                                                                     aTTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCGTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCACCAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTc                                           >  5:16641/1‑139 (MQ=255)                                                                                          atatTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCt                                       <  8:236743/138‑1 (MQ=255)                                                                                                  gCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTcc                              <  3:188053/139‑1 (MQ=255)                                                                                                    aCGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAg                            <  3:4547/139‑1 (MQ=255)                                                                                                                 tgatgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg               <  6:54011/139‑1 (MQ=255)                                                                                                                  gatgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCCCCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa              >  2:254599/1‑139 (MQ=255)                                                                                                                  gatgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa              >  5:259625/1‑139 (MQ=255)                                                                                                                  gatgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGa              >  5:148959/1‑139 (MQ=255)                                                                                                                   atgCATAAACACAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTGCCATTCTTTTATCGTCAGCTCAGAAGATCCACATGCCACCAGCGGATCCGCAGGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  3:314571/139‑1 (MQ=255)                                                                                                                   atgCATAAAAAAAGACCCTT‑A‑‑G‑GTGT‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  7:126061/139‑1 (MQ=255)                                                                                                                   atgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  1:273496/139‑1 (MQ=255)                                                                                                                    tgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             <  5:278016/138‑1 (MQ=255)                                                                                                                    tgCATAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt             >  6:278016/1‑138 (MQ=255)                                                                                                                       aTAAAAAAAGACGCTT‑T‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGGCAGCTCAGCAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa         <  5:220388/139‑1 (MQ=255)                                                                                                                       aTAAAAAAAGACCCTTAA‑‑G‑G‑GT‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa         <  3:201502/139‑1 (MQ=255)                                                                                                                        tAAAAAAAGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACa         >  7:161801/1‑138 (MQ=255)                                                                                                                            aaaaGACCCTT‑A‑‑GTG‑GT‑CTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGAGCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTG‑ATCTGCTTCGATGACATACGCt   <  1:79057/139‑1 (MQ=255)                                                                                                                            aaaaGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGc    <  7:186281/139‑1 (MQ=255)                                                                                                                              aaGACCCTT‑A‑‑G‑G‑GGTCTTTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTc  <  4:32047/139‑1 (MQ=255)                                                                                                                                                |                                                                                                                              AGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTT‑A‑‑G‑G‑G‑‑C‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTC  >  BS168_reference_genome/1317015‑1317275

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: ‑