Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,186,228	T→C	36.0%	T129T (ACA→ACG)	rsbW ←	anti‑sigma B factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,186,228	0	T	C	36.0%	15.7 / 21.4	28	T129T (ACA→ACG)	rsbW	anti‑sigma B factor
Reads supporting (aligned to +/- strand):  ref base T (13/5);  new base C (6/4);  total (19/9)
Fisher's exact test for biased strand distribution p-value = 6.77e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.00e-01

TGGTGTTCTTTAATCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTATCAGAA  >  CP000730/2186090‑2186366                                                                                                                                            |                                                                                                                                           gggTGTTCTTTAATCCATAGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTCTATACTTATGCATACTGCACGCAAGCCCACATTCGTTATATACtgt                                                                                                                                          >  2:5227/2‑141 (MQ=255)             aTCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCAt                                                                                                                              <  1:380106/141‑1 (MQ=255)                         aTTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCgtt                                                                                                                  >  1:1410/1‑139 (MQ=255)                         aTTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGAt                                                                                                                  >  1:160491/1‑141 (MQ=255)                              cTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTaaaa                                                                                                             >  1:262299/1‑141 (MQ=255)                                        aTTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGCTTGCCTCACCATAGTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAg                                                                                                   >  1:188555/1‑141 (MQ=255)                                           ttcttAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACTCCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGcc                                                                                                <  2:208376/138‑1 (MQ=255)                                            cATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGCTTAAAAATAAACCTAGGCCa                                                                                               >  1:46692/1‑141 (MQ=255)                                                    gATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTcgcg                                                                                       <  2:224372/141‑1 (MQ=255)                                                            ctctTTCGCCATTATTTCG‑ACTGGTCTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGt                                                                               >  1:392862/1‑141 (MQ=255)                                                                        tattTCGCCCCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGt                                                                   <  1:313100/141‑1 (MQ=255)                                                                        tatctcgtcacTG‑CTCTTTTTTTAGATACTGAGGCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCTCCTTCGCGTAAAAAGTCTATATTTTCGt                                                                   <  2:209323/131‑1 (MQ=255)                                                                          tttCGCACCTG‑CTCTTATTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCt                                                                 >  1:234584/1‑141 (MQ=255)                                                                                        ctTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTTAGGAc                                                    >  1:261565/1‑141 (MQ=255)                                                                                           tttttATATACTTAATCATACTGATTATCACACCAGATTCTTTATACACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTa                                                 <  2:233225/141‑1 (MQ=255)                                                                                              ttATATACTTAGTCATACTGATTATCACACCAGATTCTTTATGTACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCCCCTTCGCCTCAAAACGCTATATTTTCGTCATTATCATTAGGACCTActt                                              >  2:225503/1‑141 (MQ=255)                                                                                                 tataCTTAATCATACTGCTTGTGTCACCTTAGTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTg                                           >  1:192016/1‑141 (MQ=255)                                                                                                     cTTAGTCATACTGATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTACGACCCTATTTTTGAttt                                       >  2:63502/1‑141 (MQ=255)                                                                                                         gTCATACTGATTGTCACACCAGATTCTTTATATACTGTGAATTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATCTTTGATTCAgtt                                   <  1:279566/141‑1 (MQ=255)                                                                                                                 gATTGTCATACCTGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATa                           <  2:308911/141‑1 (MQ=255)                                                                                                                 gATTGTCACACCAGATTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATa                           <  2:314746/141‑1 (MQ=255)                                                                                                                       cacaCCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCaaa                     >  1:384905/1‑141 (MQ=255)                                                                                                                           ccAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGAACCTATTTTTAATTTAGTTGTTTTCTAATCAAAAcgg                 >  1:148363/1‑139 (MQ=255)                                                                                                                           ccAGAAACTTTATATACTGTGACTTCATCACTTAGAGATTCGCTTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCATCTTCATCATCCGTACCTATTTTTGATTTAGTTGTTTCATAATCAGAACTg                 >  2:140552/1‑141 (MQ=255)                                                                                                                               aTTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCAc             >  2:87868/1‑141 (MQ=255)                                                                                                                               aTTCTTTATATACCGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCAc             >  2:70407/1‑141 (MQ=255)                                                                                                                                     tatataCTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAt       >  1:385164/1‑141 (MQ=255)                                                                                                                                     tatataCTGTGACTTCATCCAGTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTAt       >  1:310214/1‑141 (MQ=255)                                                                                                                                          ccTGTGACTTCATCCCTTAAAGATTCGATTAAAAATAAACCTACACCACCTACGCGTAAAAACACTATCTTTTCGTCTTTATCGTAAGGCCCTATTTTCGATTTCGTTGTTTAATATTCACACCTATCACCtcgttcacca  >  2:71671/2‑132 (MQ=255)                                                                                                                                            |                                                                                                                                           TGGTGTTCTTTAATCCATTGGTTAATTTGCTCAGGTGAAATTTCATTAGCTGATTTCGACTCTTTCGCCATTATTTCGCACCTG‑CTCTTTTTTTATATACTTAGTCATACTGATTGTCACACCAGATTCTTTATATACTGTGACTTCATCCATTAAAGATTCGATTAAAAATAAACCTAGGCCACCTTCGCGTAAAAAGTCTATATTTTCGTCTTTATCGTAAGGACCTATTTTTGATTTAGTTGTTTCATAATCAAAACTGTCACCTTTATCAGAA  >  CP000730/2186090‑2186366

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑